core — API Reference

API reference for the core package.

Functions & Classes

Symbol	Kind	Description
`initLogger()`	function	Initialize the root logger. Call once at startup. Uses pino-roll for automat…
`getLogger()`	function	Get a child logger bound to a subsystem name. Safe to call before initLogger…
`getLogDir()`	function	Get the current log directory path. Useful for read APIs that need to scan lo…
`closeLogger()`	function	Flush and close the logger. Call during graceful shutdown. Returns a Promise…
`getPlatformPaths()`	function	Get OS-appropriate paths for CLEO’s global directories. Cached after first ca…
`getSystemInfo()`	function	Get a cached system information snapshot. Captured once and reused for the pr…
`_resetPlatformPathsCache()`	function	Invalidate the path and system info caches. Use in tests after mutating CLEO_…
`isProjectInitialized()`	function	Check if a CLEO project is initialized at the given root. Checks for tasks.db.
`getCleoHome()`	function	Get the global CLEO home directory. Respects CLEO_HOME env var; otherwise use…
`getCleoTemplatesDir()`	function	Get the global CLEO templates directory.
`getCleoSchemasDir()`	function	Get the global CLEO schemas directory.
`getCleoDocsDir()`	function	Get the global CLEO docs directory.
`getCleoDir()`	function	Get the project CLEO data directory (relative). Respects CLEO_DIR env var, de…
`getCleoDirAbsolute()`	function	Get the absolute path to the project CLEO directory.
`getProjectRoot()`	function	Get the project root from the CLEO directory. Respects CLEO_ROOT env var, the…
`resolveProjectPath()`	function	Resolve a project-relative path to an absolute path.
`getTaskPath()`	function	Get the path to the project’s tasks.db file (SQLite database).
`getConfigPath()`	function	Get the path to the project’s config.json file.
`getSessionsPath()`	function	Get the path to the project’s sessions.json file.
`getArchivePath()`	function	Get the path to the project’s archive file.
`getLogPath()`	function	Get the path to the project’s log file. Canonical structured runtime log path…
`getBackupDir()`	function	Get the backup directory for operational backups.
`getGlobalConfigPath()`	function	Get the global config file path.
`getCleoGlobalRecipesDir()`	function	Get the Global Justfile Hub directory. The hub stores cross-project recipe l…
`getCleoGlobalJustfilePath()`	function	Get the absolute path to the primary global justfile.
`getCleoPiExtensionsDir()`	function	Get the Global Pi Extensions Hub directory. Houses the Pi extensions that dr…
`getCleoCantWorkflowsDir()`	function	Get the Global CANT Workflows Hub directory. Stores compiled and parsed…
`getCleoGlobalAgentsDir()`	function	Get the Global CLEO Agents directory. Holds globally-available CANT agent de…
`getAgentOutputsDir()`	function	Get the agent outputs directory (relative path) from config or default. Conf…
`getAgentOutputsAbsolute()`	function	Get the absolute path to the agent outputs directory.
`getManifestPath()`	function	Get the absolute path to the legacy agent-outputs flat-file (deprecated per ADR-027). Checks config.agentOutputs…
`getManifestArchivePath()`	function	Get the absolute path to the MANIFEST.archive.jsonl file.
`isAbsolutePath()`	function	Check if a path is absolute (POSIX or Windows).
`getCleoLogDir()`	function	Get the OS log directory for CLEO global logs. Linux: ~/.local/state/cleo \| m…
`getCleoCacheDir()`	function	Get the OS cache directory for CLEO. Linux: ~/.cache/cleo \| macOS: ~/Library/…
`getCleoTempDir()`	function	Get the OS temp directory for CLEO ephemeral files.
`getCleoConfigDir()`	function	Get the OS config directory for CLEO. Linux: ~/.config/cleo \| macOS: ~/Librar…
`getCleoTemplatesTildePath()`	function	Get the CLEO templates directory as a tilde-prefixed path for use in `@` refe…
`getAgentsHome()`	function	Get the global agents hub directory. Respects AGENTS_HOME env var, defaults t…
`getClaudeAgentsDir()`	function	Get the Claude Code agents directory (~/.claude/agents by default).
`getClaudeMemDbPath()`	function	Get the claude-mem SQLite database path.
`tableExists()`	function	Check whether a table exists in a SQLite database.
`isSqliteBusy()`	function	Check if an error is a SQLite BUSY error (database locked by another process)…
`createSafetyBackup()`	function	Create a pre-migration safety backup of the database file. Only creates the…
`reconcileJournal()`	function	Bootstrap and reconcile the Drizzle migration journal. Handles three scenari…
`migrateWithRetry()`	function
`ensureColumns()`	function	Ensure all required columns exist on a table. Uses PRAGMA table_info to insp…
`vacuumIntoBackup()`	function	Create a VACUUM INTO snapshot of the SQLite database. Debounced by default (…
`listSqliteBackups()`	function	List existing SQLite backup snapshots, newest first.
`getBrainDbPath()`	function	Get the path to the brain.db SQLite database file.
`resolveBrainMigrationsFolder()`	function	Resolve the path to the drizzle-brain migrations folder. Works from both src/…
`isBrainVecLoaded()`	function	Check whether the sqlite-vec extension is loaded for the current brain.db.
`getBrainDb()`	function	Initialize the brain.db SQLite database (lazy, singleton). Creates the databa…
`closeBrainDb()`	function	Close the brain.db database connection and release resources.
`resetBrainDbState()`	function	Reset brain.db singleton state without saving. Used during tests or when data…
`getBrainNativeDb()`	function	Get the underlying node:sqlite DatabaseSync instance for brain.db. Useful for…
`getNexusDbPath()`	function	Get the path to the nexus.db SQLite database file. nexus.db lives in the glob…
`resolveNexusMigrationsFolder()`	function	Resolve the path to the drizzle-nexus migrations folder. Works from both src/…
`getNexusDb()`	function	Initialize the nexus.db SQLite database (lazy, singleton). Creates the databa…
`closeNexusDb()`	function	Close the nexus.db database connection and release resources.
`resetNexusDbState()`	function	Reset nexus.db singleton state without saving. Used during tests or when data…
`getNexusNativeDb()`	function	Get the underlying node:sqlite DatabaseSync instance for nexus.db. Useful for…
`openNativeDatabase()`	function	Open a node:sqlite DatabaseSync with CLEO standard pragmas. CRITICAL: WAL mo…
`getDbPath()`	function	Get the path to the SQLite database file.
`getDb()`	function	Initialize the SQLite database (lazy, singleton). Creates the database file a…
`resolveMigrationsFolder()`	function	Resolve the path to the drizzle migrations folder. Works from both src/ (dev…
`closeDb()`	function	Close the database connection and release resources.
`resetDbState()`	function	Reset database singleton state without saving. Used during migrations when da…
`getSchemaVersion()`	function	Get the schema version from the database.
`dbExists()`	function	Check if the database file exists.
`getNativeDb()`	function	Get the underlying node:sqlite DatabaseSync instance. Useful for direct PRAGM…
`getNativeTasksDb()`	function	Get the underlying node:sqlite DatabaseSync instance for tasks.db. Alias for…
`closeAllDatabases()`	function	Close ALL database singletons (tasks.db, brain.db, nexus.db). Must be called…
`safeParseJson()`	function	Parse a JSON string, returning undefined on null/undefined input or parse error.
`safeParseJsonArray()`	function	Parse a JSON string expected to contain an array. Returns undefined for null/…
`rowToTask()`	function	Convert a database TaskRow to a domain Task object.
`taskToRow()`	function	Convert a domain Task to a database row for insert/upsert.
`archivedTaskToRow()`	function	Convert a domain Task to a row suitable for archived tasks.
`rowToSession()`	function	Convert a SessionRow to a domain Session.
`getSignaldockDbPath()`	function	Get the path to the signaldock.db SQLite database file.
`ensureSignaldockDb()`	function	Ensure signaldock.db exists and has the full schema applied. Idempotent — sa…
`checkSignaldockDbHealth()`	function	Check signaldock.db health — table count, WAL mode, schema version. Used by…
`cleanupBrainRefsOnTaskDelete()`	function	Clean up brain.db references after a task is deleted from tasks.db. Handles:…
`cleanupBrainRefsOnSessionDelete()`	function	Clean up brain.db references after a session is deleted from tasks.db. Handl…
`taskExistsInTasksDb()`	function	Verify a task ID exists in tasks.db before writing a cross-DB reference to br…
`reconcileOrphanedRefs()`	function	Reconcile orphaned cross-DB references in brain.db. Scans brain.db for refer…
`sessionExistsInTasksDb()`	function
`agentExistsInSignaldockDb()`	function	Verify an agent exists in signaldock.db before creating cross-DB references…
`getErrorDefinition()`	function	Look up an error definition by exit code.
`getErrorDefinitionByLafsCode()`	function	Look up an error definition by LAFS string code.
`getAllErrorDefinitions()`	function	Get all error definitions as an array.
`CleoError`	class	Structured error class for CLEO operations. Carries an exit code, human-reada…
`upsertTask()`	function	Upsert a single task row into the tasks table. Handles both active task upser…
`upsertSession()`	function	Upsert a single session row into the sessions table.
`updateDependencies()`	function	Update dependencies for a task: delete existing, then re-insert. Optionally f…
`batchUpdateDependencies()`	function	Batch-update dependencies for multiple tasks in two bulk SQL operations. Repl…
`loadDependenciesForTasks()`	function	Batch-load dependencies for a list of tasks and apply them in-place. Uses inA…
`loadRelationsForTasks()`	function	Batch-load relations for a list of tasks and apply them in-place. Mirrors loa…
`generateAgentId()`	function	Generate a unique agent instance ID. Format: `agt_{YYYYMMDDHHmmss}_{6hex}`
`registerAgent()`	function	Register a new agent instance in the database. Sets initial status to ‘starti…
`deregisterAgent()`	function	Deregister (stop) an agent instance. Sets status to ‘stopped’ and records the…
`heartbeat()`	function	Record a heartbeat for an agent instance. Updates `last_heartbeat` and return…
`updateAgentStatus()`	function	Update agent status with optional error tracking. When status is ‘error’ or ’…
`incrementTasksCompleted()`	function	Increment the completed task count for an agent.
`listAgentInstances()`	function	List agent instances with optional filters.
`getAgentInstance()`	function	Get a single agent instance by ID.
`classifyError()`	function	Classify an error as retriable, permanent, or unknown. Retriable errors are…
`getAgentErrorHistory()`	function	Get the error history for a specific agent.
`checkAgentHealth()`	function	Check agent health by finding instances whose last heartbeat exceeds the thre…
`markCrashed()`	function	Mark an agent instance as crashed. Increments error count and sets status to…
`getHealthReport()`	function	Generate a health report summarizing all agent instances. Includes counts by…
`setMetaValue()`	function	Write a JSON blob to the schema_meta table by key.
`createSqliteDataAccessor()`	function	Create a SQLite-backed DataAccessor. Opens (or creates) the SQLite database…
`atomicWrite()`	function	Write data to a file atomically. Creates parent directories if they don’t exi…
`safeReadFile()`	function	Read a file and return its contents. Returns null if the file does not exist.
`atomicWriteJson()`	function	Write JSON data atomically with consistent formatting.
`atomicDatabaseMigration()`	function	Perform atomic database migration using rename operations. Pattern: 1. Wri…
`restoreDatabaseFromBackup()`	function	Restore database from backup after failed migration.
`cleanupMigrationArtifacts()`	function	Clean up migration artifacts after successful migration.
`validateSqliteDatabase()`	function	Validate SQLite database integrity by attempting to open it.
`createBackup()`	function	Create a numbered backup of a file. Rotates existing backups (file.1 - file.2…
`listBackups()`	function	List existing backups for a file, sorted by number (newest first).
`restoreFromBackup()`	function	Restore a file from its most recent backup. Returns the path of the backup th…
`acquireLock()`	function	Acquire an exclusive lock on a file. Returns a release function that must be…
`isLocked()`	function	Check if a file is currently locked.
`withLock()`	function	Execute a function while holding an exclusive lock on a file. The lock is aut…
`isProviderHookEvent()`	function	Type guard for CAAMP/provider-discoverable canonical hook events.
`isInternalHookEvent()`	function	Type guard for CLEO-local coordination hook events.
`HookRegistry`	class	Central registry for hook handlers. Manages registration, priority-based ord…
`readJson()`	function	Read and parse a JSON file. Returns null if the file does not exist.
`readJsonRequired()`	function	Read a JSON file, throwing if it doesn’t exist.
`computeChecksum()`	function	Compute a truncated SHA-256 checksum of a value. Used for integrity verificat…
`saveJson()`	function	Save JSON data with optional locking, backup, and validation. Follows the CLE…
`appendJsonl()`	function	Append a line to a JSONL file atomically. Used for manifest entries and audit…
`readLogEntries()`	function	Read log entries from a hybrid JSON/JSONL file. Handles three formats: 1. P…
`makeCleoGitEnv()`	function	Build environment variables that point git at the isolated .cleo/.git repo…
`cleoGitCommand()`	function	Run a git command against the isolated .cleo/.git repo, suppressing errors…
`isCleoGitInitialized()`	function	Check whether the isolated .cleo/.git repo has been initialized. T4872
`loadStateFileAllowlist()`	function	Load additional state file paths from config.json…
`loadCheckpointConfig()`	function	Load checkpoint configuration from config.json. T4552
`shouldCheckpoint()`	function	Check whether a checkpoint should be performed. Evaluates: enabled, .cleo/.gi…
`gitCheckpoint()`	function	Stage .cleo/ state files and commit to the isolated .cleo/.git repo. Never fa…
`gitCheckpointStatus()`	function	Show checkpoint configuration and status. T4552 T4872
`gitCheckpointDryRun()`	function	Show what files would be committed (dry-run). T4552 T4872
`DataSafetyError`	class	Safety violation error
`getSafetyStats()`	function	Get current safety statistics
`resetSafetyStats()`	function	Reset safety statistics (for testing)
`safeSaveSessions()`	function	Safe wrapper for DataAccessor.saveSessions()
`safeSaveArchive()`	function	Safe wrapper for DataAccessor.saveArchive()
`safeSingleTaskWrite()`	function	Safe wrapper for single-task write operations (T5034). Performs: 1. Sequence…
`safeAppendLog()`	function	Safe wrapper for DataAccessor.appendLog() Note: Log appends are fire-and-for…
`runDataIntegrityCheck()`	function	Run comprehensive data integrity check. Validates all data files and sequence…
`forceSafetyCheckpoint()`	function	Force immediate checkpoint. Use before destructive operations.
`disableSafety()`	function	Disable all safety for current process. DANGEROUS - only use for recovery ope…
`enableSafety()`	function	Re-enable safety after being disabled.
`SafetyDataAccessor`	class	Safety-enabled DataAccessor wrapper. Wraps any DataAccessor implementation a…
`wrapWithSafety()`	function	Wrap a DataAccessor with safety. This is the internal factory helper that wr…
`isSafetyEnabled()`	function	Check if safety is currently enabled.
`getSafetyStatus()`	function	Get safety status information.
`createDataAccessor()`	function	Create a DataAccessor for the given working directory. Always creates a SQLit…
`getAccessor()`	function	Convenience: get a DataAccessor with auto-detected engine.
`showSequence()`	function	Show current sequence state.
`checkSequence()`	function	Check sequence integrity.
`repairSequence()`	function	Repair sequence if behind.
`allocateNextTaskId()`	function	Atomically allocate the next task ID via SQLite. Uses BEGIN IMMEDIATE to gua…
`SafetyError`	class	Safety violation error.
`checkTaskExists()`	function	Check if a task ID already exists (collision detection).
`verifyTaskWrite()`	function	Verify a task was actually written to the database.
`validateAndRepairSequence()`	function	Validate and repair sequence if necessary.
`triggerCheckpoint()`	function	Trigger auto-checkpoint after successful write.
`safeCreateTask()`	function	Safely create a task with all safety mechanisms. Wraps the actual createTask…
`safeUpdateTask()`	function	Safely update a task with all safety mechanisms.
`safeDeleteTask()`	function	Safely delete a task with all safety mechanisms.
`verifySessionWrite()`	function	Verify session write.
`safeCreateSession()`	function	Safely create a session with all safety mechanisms.
`forceCheckpointBeforeOperation()`	function	Force a checkpoint before destructive operations. Use this before migrations,…
`runDataIntegrityCheck()`	function	Run comprehensive data integrity check. Reports all issues found.
`getTask()`	function	Get a task by ID, including its dependencies.
`updateTask()`	function	Update an existing task.
`deleteTask()`	function	Delete a task by ID.
`listTasks()`	function	List tasks with optional filters.
`findTasks()`	function	Find tasks by fuzzy text search.
`archiveTask()`	function	Archive a task (sets status to ‘archived’ with metadata).
`addDependency()`	function	Add a dependency between tasks.
`removeDependency()`	function	Remove a dependency.
`addRelation()`	function	Add a relation between tasks.
`getRelations()`	function	Get relations for a task.
`getBlockerChain()`	function	Get the dependency chain (blockers) for a task using recursive CTE.
`getChildren()`	function	Get children of a task (hierarchy).
`getSubtree()`	function	Build a tree from a root task using recursive CTE.
`countByStatus()`	function	Count tasks by status.
`countTasks()`	function	Get total task count (excluding archived).
`createTask()`	function	Create a task with full safety protections. Includes: collision detection, wr…
`updateTaskSafe()`	function	Update a task with full safety protections. Includes: write verification, aut…
`deleteTaskSafe()`	function	Delete a task with full safety protections. Includes: delete verification, au…
`taskShowNext()`	function	Build `_next` directives for a full task detail result (tasks.show).
`taskListItemNext()`	function	Build `_next` directives for a task in a list or find result.
`sessionListItemNext()`	function	Build `_next` directives for a session in a list or find result.
`sessionStartNext()`	function	Build `_next` directives for a session start result.
`memoryFindHitNext()`	function	Build `_next` directives for a memory search (find) hit.
`showTask()`	function	Get a task by ID with enriched details. Checks active tasks first, then archi…
`createPage()`	function	Create an LAFSPage object from pagination parameters. Returns mode:“none” wh…
`paginate()`	function	Apply pagination to an array of items and return the sliced result with page…
`toCompact()`	function	Convert a full Task to compact representation with _next directives.
`listTasks()`	function	List tasks with optional filtering and pagination. T4460
`fuzzyScore()`	function	Calculate fuzzy match score between query and text. Higher score = better mat…
`findTasks()`	function	Search tasks by fuzzy matching, ID prefix, or exact title. Returns minimal fi…
`extractAdrId()`	function	Extract ADR ID from filename (e.g., ‘ADR-007-domain-consolidation.md’ - ‘ADR-…
`parseFrontmatter()`	function	Parse bold-key frontmatter pattern: Key: value
`extractTitle()`	function	Extract H1 title from markdown
`parseAdrFile()`	function	Parse a single ADR markdown file into an AdrRecord
`linkPipelineAdr()`	function	Link ADRs to a pipeline task when the architecture_decision stage completes.
`syncAdrsToDb()`	function	Sync all ADR markdown files into the architecture_decisions table AND regener…
`recordEvidence()`	function	Record an evidence artifact linked to a lifecycle stage. Writes to the SQLit…
`getEvidence()`	function	Query evidence records for an epic, optionally filtered by stage.
`linkProvenance()`	function	Convenience wrapper to record a file as provenance evidence. Converts the fi…
`getEvidenceSummary()`	function	Aggregate evidence counts per stage for an epic.
`normalizeEpicId()`	function	Strip suffixes from epic directory names. E.g. `T4881_install-channels` -…
`getRcasdBaseDir()`	function	Get the absolute path to the `.cleo/rcasd/` base directory.
`getEpicDir()`	function	Get the absolute path to `.cleo/rcasd/{epicId}/`. Uses the normalized epic ID…
`findEpicDir()`	function	Search both `rcasd/` and legacy `rcsd/` for an existing epic directory. Also…
`getStagePath()`	function	Get the stage subdirectory path for an epic. Uses STAGE_SUBDIRS mapping, fall…
`ensureStagePath()`	function	Get the stage subdirectory path, creating it if it does not exist.
`getManifestPath()`	function	Get the manifest path for an epic under the default rcasd directory.
`findManifestPath()`	function	Search both `rcasd/` and `rcsd/` for an existing manifest file. Checks suffix…
`getLooseResearchFiles()`	function	Scan the rcasd root directory for loose `T####_*.md` files that are not insid…
`listEpicDirs()`	function	List all epic directories across `rcasd/` and `rcsd/`.
`parseFrontmatter()`	function	Parse YAML frontmatter from a markdown string. Finds the YAML block delimite…
`serializeFrontmatter()`	function	Convert a FrontmatterMetadata object to a YAML frontmatter string. Output fo…
`addFrontmatter()`	function	Add or replace YAML frontmatter in markdown content. If the content already…
`buildFrontmatter()`	function	Convenience builder for common frontmatter patterns. Auto-sets `updated` to…
`getBacklinks()`	function	Scan all markdown files in `.cleo/rcasd/` for files that reference the given…
`getStageOrder()`	function	Get the order/index of a stage (1-based).
`isStageBefore()`	function	Check if stage A comes before stage B in the pipeline.
`isStageAfter()`	function	Check if stage A comes after stage B in the pipeline.
`getNextStage()`	function	Get the next stage in the pipeline.
`getPreviousStage()`	function	Get the previous stage in the pipeline.
`getStagesBetween()`	function	Get all stages between two stages (inclusive).
`getPrerequisites()`	function	Get prerequisites for a stage.
`isPrerequisite()`	function	Check if one stage is a prerequisite of another.
`getDependents()`	function	Get all stages that depend on a given stage.
`isValidStage()`	function	Check if a stage name is valid.
`validateStage()`	function	Validate a stage name and throw if invalid.
`isValidStageStatus()`	function	Check if a stage status is valid.
`getStagesByCategory()`	function	Get stages by category.
`getSkippableStages()`	function	Get skippable stages.
`checkTransition()`	function	Check if a transition is allowed.
`ensureStageArtifact()`	function	Ensure stage artifact exists and frontmatter/backlinks are up to date.
`getSkillSearchPaths()`	function	Build the CAAMP skill search paths in priority order. Uses CAAMP’s canonical…
`getSkillsDir()`	function	Get the primary skills directory (app-embedded). T4516
`getSharedDir()`	function	Get the shared skills resources directory. T4516
`mapSkillName()`	function	Map a user-friendly skill name to the canonical ct-prefixed directory name. S…
`listCanonicalSkillNames()`	function	List all known canonical skill names (unique values from the map). T4516
`parseFrontmatter()`	function	Parse YAML-like frontmatter from a SKILL.md file. Handles the --- delimited h…
`discoverSkill()`	function	Discover a single skill from a directory. Tries CAAMP’s parseSkillFile first,…
`discoverSkillsInDir()`	function	Discover all skills in a single directory. Scans for subdirectories containin…
`discoverAllSkills()`	function	Discover all skills across CAAMP search paths. Returns skills in priority ord…
`findSkill()`	function	Find a specific skill by name across all search paths. T4516
`toSkillSummary()`	function	Convert a Skill to a lightweight SkillSummary. T4516
`generateManifest()`	function	Generate a skill manifest from discovered skills. T4516
`resolveTemplatePath()`	function	Resolve a skill template path (SKILL.md) by name. T4516
`loadPlaceholders()`	function	Load token definitions from placeholders.json. T4521
`buildDefaults()`	function	Build the full default values map (merging placeholders.json with hardcoded d…
`validateTokenValue()`	function	Validate a single token value against its pattern. T4521
`validateRequired()`	function	Validate all required tokens are present and valid. T4521
`validateAllTokens()`	function	Validate all tokens in a values map (required + optional). T4521
`injectTokens()`	function	Inject token values into a template string. Replaces all TOKEN_NAME patterns…
`hasUnresolvedTokens()`	function	Check if a template has unresolved tokens after injection. T4521
`loadAndInject()`	function	Load a skill template and inject tokens. T4521
`setFullContext()`	function	Build a complete TokenValues map from a task, resolving all standard tokens…
`autoDispatch()`	function	Auto-dispatch a task to the most appropriate skill. Tries strategies in prior…
`dispatchExplicit()`	function	Dispatch with explicit skill override. Verifies the skill exists before retur…
`getProtocolForDispatch()`	function	Get the protocol type for a dispatch result. T4517
`prepareSpawnContext()`	function	Prepare spawn context for a dispatched skill. Returns the skill name and prot…
`prepareSpawnMulti()`	function	Compose multiple skills into a single prompt with progressive disclosure. Por…
`buildStageGuidance()`	function	Build structured stage guidance for a given pipeline stage. Resolves the pri…
`formatStageGuidance()`	function	Format stage guidance as a Markdown-wrapped system prompt. Since…
`renderStageGuidance()`	function	Convenience wrapper: build AND format in a single call.
`getLifecycleState()`	function	Get the current lifecycle state for an epic. T4467
`startStage()`	function	Start a lifecycle stage. T4467
`completeStage()`	function	Complete a lifecycle stage. T4467
`skipStage()`	function	Skip a lifecycle stage. T4467
`checkGate()`	function	Check lifecycle gate before starting a stage. T4467
`getLifecycleStatus()`	function	Get lifecycle status for an epic from SQLite. Returns stage progress, current…
`getLifecycleHistory()`	function	Get lifecycle history for an epic. Returns stage transitions and gate events…
`getLifecycleGates()`	function	Get all gate statuses for an epic. T4785
`getStagePrerequisites()`	function	Get prerequisites for a target stage. Pure data function, no I/O. T4785
`checkStagePrerequisites()`	function	Check if a stage’s prerequisites are met for an epic. T4785
`recordStageProgress()`	function	Record a stage status transition (progress/record). SQLite-native implementat…
`skipStageWithReason()`	function	Skip a stage with a reason (engine-compatible). T4785
`resetStage()`	function	Reset a stage to pending (emergency). T4785
`passGate()`	function	Mark a gate as passed. SQLite-native implementation - T4801 T4785 T4801
`failGate()`	function	Mark a gate as failed. SQLite-native implementation - T4801 T4785 T4801
`listEpicsWithLifecycle()`	function	List all epic IDs that have lifecycle data. T4785
`getCurrentSessionId()`	function	Get the current session ID.
`getContextStatePath()`	function	Get context state file path for a session.
`readContextState()`	function	Read context state for a session. Returns null if stale or missing.
`getThresholdLevel()`	function	Determine the threshold level for a given percentage.
`shouldAlert()`	function	Determine if we should alert based on threshold crossing. Returns the alert l…
`getRecommendedAction()`	function	Get recommended action for an alert level.
`checkContextAlert()`	function	Main function to check and determine if an alert should fire. Non-blocking -…
`pushWarning()`	function	Push a deprecation or informational warning into the current envelope. Warnin…
`formatSuccess()`	function	Format a successful result as a full LAFS-conformant envelope. Always produc…
`formatError()`	function	Format an error as a full LAFS-conformant envelope. Always produces the full…
`formatOutput()`	function	Format any result (success or error) as LAFS JSON.
`getRegistryEntry()`	function	Look up a registry entry by CLEO exit code. T4671 T4663
`getRegistryEntryByLafsCode()`	function	Look up a registry entry by LAFS string code. T4671 T4663
`getCleoErrorRegistry()`	function	Get the full CLEO error registry for conformance testing. T4671 T4663
`isCleoRegisteredCode()`	function	Check if a LAFS code is registered in the CLEO error registry. T4671 T4663
`createTestDb()`	function	Create a temporary directory with an initialized tasks.db. Usage:
`makeTasks()`	function	Build full Task objects from a list of task partials. Useful for seeding test…
`seedTasks()`	function	Seed tasks into the test database via the accessor. Uses a two-pass approach…
`getChildren()`	function	Get direct children of a task.
`getChildIds()`	function	Get direct child IDs.
`getDescendants()`	function	Get all descendants of a task (recursive).
`getDescendantIds()`	function	Get all descendant IDs (flat list).
`getParentChain()`	function	Get the parent chain (ancestors) from a task up to the root. Returns ordered…
`getParentChainIds()`	function	Get the parent chain as IDs.
`getDepth()`	function	Calculate depth of a task in the hierarchy (0-based). Root tasks have depth 0…
`getRootAncestor()`	function	Get the root ancestor of a task.
`isAncestorOf()`	function	Check if a task is an ancestor of another.
`isDescendantOf()`	function	Check if a task is a descendant of another.
`getSiblings()`	function	Get sibling tasks (same parent).
`validateHierarchy()`	function
`wouldCreateCircle()`	function	Detect circular reference if parentId were set.
`buildTree()`	function
`flattenTree()`	function	Flatten a tree back to a list (depth-first).
`resolveHierarchyPolicy()`	function	Resolve a full HierarchyPolicy from config, starting with a profile preset an…
`assertParentExists()`	function	Assert that a parent task exists in the task list. Returns an error result if…
`assertNoCycle()`	function	Assert that re-parenting would not create a cycle. Returns an error result if…
`countActiveChildren()`	function	Count active (non-done, non-cancelled, non-archived) children of a parent.
`validateHierarchyPlacement()`	function	Validate whether a new task can be placed under the given parent according to…
`loadConfig()`	function	Load and merge configuration from all sources. Priority: defaults global con…
`getConfigValue()`	function	Get a single config value with source tracking. Returns the value and which s…
`getRawConfigValue()`	function	Get a raw config value from the project config file only (no cascade). Return…
`getRawConfig()`	function	Get the full raw project config (no cascade). Returns null if no config file…
`parseConfigValue()`	function	Parse a string value into its appropriate JS type. Handles booleans, null, in…
`setConfigValue()`	function	Set a config value in the project or global config file (dot-notation support…
`applyStrictnessPreset()`	function	Apply a strictness preset to the project (or global) config. Merges preset va…
`listStrictnessPresets()`	function	List all available presets with their descriptions and values. Used by the CL…
`isMissingBrainSchemaError()`	function	Return true when the error is the “no such table: brain_*” SQLite error throw…
`isAutoCaptureEnabled()`	function	Return true when `brain.autoCapture` is enabled for the given project. Resol…
`recordDecision()`	function	Record a decision to the audit trail. Appends a JSON line to…
`getDecisionLog()`	function	Read the decision log, optionally filtered by sessionId and/or taskId.
`computeHandoff()`	function	Compute handoff data for a session. Gathers all session statistics and auto-c…
`persistHandoff()`	function	Persist handoff data to a session.
`getHandoff()`	function	Get handoff data for a session.
`getLastHandoff()`	function	Get handoff data for the most recent ended session. Filters by scope if provi…
`computeDebrief()`	function	Compute rich debrief data for a session. Builds on computeHandoff() and adds…
`BrainDataAccessor`	class
`getBrainAccessor()`	function	Factory: get a BrainDataAccessor backed by the brain.db singleton.
`typedAll()`	function	Type-safe wrapper for `StatementSync.all` — centralizes the `as unknown as` c…
`typedGet()`	function	Type-safe wrapper for `StatementSync.get` — centralizes the `as unknown as` c…
`LocalEmbeddingProvider`	class	Local embedding provider backed by xenova/transformers. Produces 384-dimensi…
`getLocalEmbeddingProvider()`	function	Get or create the shared LocalEmbeddingProvider singleton.
`setEmbeddingProvider()`	function	Register an embedding provider for the brain system. Validates that the provi…
`getEmbeddingProvider()`	function	Get the currently registered embedding provider, or null.
`clearEmbeddingProvider()`	function	Clear the current embedding provider (useful for testing).
`embedText()`	function	Embed text into a float vector using the registered provider. Returns null wh…
`isEmbeddingAvailable()`	function	Check whether embedding is currently available.
`initDefaultProvider()`	function	Initialize the default local embedding provider. Loads the LocalEmbeddingPro…
`searchSimilar()`	function	Search for entries similar to a query string using vector similarity. 1. Emb…
`ensureFts5Tables()`	function	Create FTS5 virtual tables and content-sync triggers if they don’t exist. Us…
`rebuildFts5Index()`	function	Rebuild FTS5 indexes from the content tables. Useful after bulk inserts that…
`searchBrain()`	function	Unified search across all BRAIN memory tables. Uses FTS5 MATCH for full-text…
`resetFts5Cache()`	function	Reset the cached FTS5 availability flag. Used in tests to force re-detection.
`hybridSearch()`	function	Hybrid search across FTS5, vector similarity, and graph neighbors. 1. Runs F…
`generateMemoryBridgeContent()`	function	Generate memory bridge content from brain.db. Returns the markdown string (do…
`writeMemoryBridge()`	function	Write memory bridge content to .cleo/memory-bridge.md.
`refreshMemoryBridge()`	function	Best-effort refresh: call from session.end, tasks.complete, or memory.observe…
`generateContextAwareContent()`	function	Generate context-aware memory bridge content and write to disk. When…
`maybeRefreshMemoryBridge()`	function	Refresh the memory bridge if autoRefresh is enabled and the debounce window h…
`searchBrainCompact()`	function	Token-efficient compact search across BRAIN tables. Returns index-level hits…
`timelineBrain()`	function	Get chronological context around an anchor entry. Fetches the anchor’s full d…
`fetchBrainEntries()`	function	Batch-fetch full details by IDs. Groups IDs by prefix to query the correct ta…
`observeBrain()`	function	Save an observation to the BRAIN observations table. Replaces the external cl…
`populateEmbeddings()`	function	Backfill embeddings for existing observations that lack them. Iterates throu…
`queryAudit()`	function	Query audit entries from SQLite audit_log table. Used by session-grade.ts for…
`storeLearning()`	function	Store a new learning. T4769, T5241
`searchLearnings()`	function	Search learnings by criteria. Results sorted by confidence (highest first)…
`learningStats()`	function	Get learning statistics. T4769, T5241
`gradeSession()`	function	Grade a session by sessionId using the 5-dimension behavioral rubric.
`readGrades()`	function	Read past grade results from .cleo/metrics/GRADES.jsonl
`isValidAdapter()`	function	Validate that a loaded module export implements the CLEOProviderAdapter inter…
`loadAdapterFromManifest()`	function	Dynamically load and instantiate an adapter from its manifest. Uses the mani…
`discoverAdapterManifests()`	function	Scan the packages/adapters/ directory for adapter packages. Each adapter must…
`detectProvider()`	function	Detect whether a provider is active in the current environment by checking it…
`AdapterManager`	class	Central adapter manager. Singleton per process. Lifecycle: 1. discover() —…
`bridgeSessionToMemory()`	function	Bridge session end data to brain.db as an observation. Builds a summary text…
`storeDecision()`	function	Store a new decision or update an existing one if a duplicate is found. Dupli…
`recallDecision()`	function	Recall a specific decision by ID. T5155
`searchDecisions()`	function	Search decisions by type, confidence, outcome, and/or free-text query. Query…
`listDecisions()`	function	List decisions with pagination. T5155
`updateDecisionOutcome()`	function	Update the outcome of a decision after learning from results. T5155
`storePattern()`	function	Store a new pattern. If a similar pattern already exists (same type + matchin…
`searchPatterns()`	function	Search patterns by criteria. T4768, T5241
`patternStats()`	function	Get pattern statistics. T4768, T5241
`extractTaskCompletionMemory()`	function	Extract and store memory entries when a task is completed. - Always stores a…
`extractSessionEndMemory()`	function	Extract and store memory entries when a session ends. - Stores a process dec…
`resolveTaskDetails()`	function	Resolve an array of task IDs to their full Task objects. Tasks that cannot be…
`extractFromTranscript()`	function	Extract key observations from a provider session transcript and store them in…
`handleSessionStart()`	function	Handle SessionStart - capture initial session context T138: Refresh memory b…
`handleSessionEnd()`	function	Handle SessionEnd - capture session summary T138: Refresh memory bridge afte…
`handleToolStart()`	function	Handle PreToolUse (maps to task.start in CLEO, canonical: was onToolStart)
`handleToolComplete()`	function	Handle PostToolUse (maps to task.complete in CLEO, canonical: was onToolCompl…
`handleError()`	function	Handle PostToolUseFailure — capture operation errors to BRAIN. Includes an i…
`handleFileChange()`	function	Handle Notification (file-change variant) - capture file changes to BRAIN Ga…
`handleSystemNotification()`	function	Handle Notification — capture system notifications as BRAIN observations. On…
`handleWorkPromptSubmit()`	function	Handle PromptSubmit — log incoming mutation intents to BRAIN. Only fires for…
`handleWorkResponseComplete()`	function	Handle ResponseComplete — capture completed mutations to BRAIN. Only fires f…
`handleSubagentStart()`	function	Handle SubagentStart — log subagent spawn as a BRAIN observation. Records th…
`handleSubagentStop()`	function	Handle SubagentStop — log subagent completion result as a BRAIN observation…
`handlePreCompact()`	function	Handle PreCompact — snapshot current session memory context to BRAIN. Fires…
`handlePostCompact()`	function	Handle PostCompact — record compaction completion to BRAIN. Fires immediatel…
`recordAssumption()`	function	Record an assumption made during a session. Appends to .cleo/audit/assumption…
`linkMemoryToTask()`	function	Link a memory entry to a task. T5156
`unlinkMemoryFromTask()`	function	Remove a link between a memory entry and a task. T5156
`getTaskLinks()`	function	Get all memory entries linked to a specific task. T5156
`getMemoryLinks()`	function	Get all tasks linked to a specific memory entry. T5156
`bulkLink()`	function	Batch create multiple links at once. T5156
`getLinkedDecisions()`	function	Get all decisions linked to a task. Convenience method that fetches full deci…
`getLinkedPatterns()`	function	Get all patterns linked to a task. Convenience method that fetches full patte…
`getLinkedLearnings()`	function	Get all learnings linked to a task. Convenience method that fetches full lear…
`extractMemoryItems()`	function	Extract memory-worthy items from debrief data. Pure function — no side effec…
`persistSessionMemory()`	function	Main entry point — called from session.end handler. Extracts memory-worthy c…
`buildSummarizationPrompt()`	function	Build a summarization prompt from debrief data. Returns a formatted prompt s…
`ingestStructuredSummary()`	function	Ingest a structured session summary directly into brain.db. Stores each fiel…
`getSessionMemoryContext()`	function	Retrieve session memory for a given scope. Used by briefing/handoff to enrich…
`depsReady()`	function	Check if all dependencies of a task are satisfied.
`initializePipeline()`	function	Initialize a new pipeline for a task. Creates a new pipeline record in the d…
`getPipeline()`	function	Retrieve a pipeline by task ID. Returns the complete pipeline state includin…
`advanceStage()`	function	Advance a pipeline to the next stage. Performs atomic stage transition with…
`getCurrentStage()`	function	Get the current stage of a pipeline. Convenience method to quickly check whi…
`listPipelines()`	function	List pipelines with optional filtering.
`completePipeline()`	function	Complete a pipeline (mark all stages done). Marks the pipeline as completed…
`cancelPipeline()`	function	Cancel a pipeline before completion. Marks the pipeline as cancelled (user-i…
`pipelineExists()`	function	Check if a pipeline exists for a task.
`getPipelineStatistics()`	function	Get pipeline statistics. Returns aggregate counts of pipelines by status and…
`getPipelineStages()`	function	Get all stages for a pipeline.
`computeBriefing()`	function	Compute the complete session briefing. Aggregates data from all 6+ sources.
`findSessions()`	function	Find sessions with minimal field projection. Loads all sessions, applies fil…
`archiveSessions()`	function	Archive old/ended sessions. Identifies ended and suspended sessions older tha…
`cleanupSessions()`	function	Remove orphaned sessions, auto-end stale active sessions, and clean up stale…
`getContextDrift()`	function	Compute context drift score for the current session. Compares session progres…
`getSessionHistory()`	function	List session history with focus changes and completed tasks. If sessionId is…
`showSession()`	function	Show a specific session. Looks in active sessions first, then session history…
`getSessionStats()`	function	Compute session statistics, optionally for a specific session. Throws CleoErr…
`suspendSession()`	function	Suspend an active session. Sets status to ‘suspended’ and records the reason…
`switchSession()`	function	Switch to a different session. Suspends the current active session and activa…
`SessionView`	class
`selectRuntimeProviderContext()`	function
`detectRuntimeProviderContext()`	function
`resetRuntimeProviderContextCache()`	function
`parseScope()`	function	Parse a scope string into a SessionScope. T4463
`readSessions()`	function	Read sessions from accessor or JSON file. T4463
`saveSessions()`	function	Save sessions via accessor or JSON file. T4463
`startSession()`	function	Start a new session. T4463
`endSession()`	function	End a session. T4463
`sessionStatus()`	function	Get current session status. T4463
`resumeSession()`	function	Resume an existing session. T4463
`listSessions()`	function	List sessions with optional filtering. T4463
`gcSessions()`	function	Garbage collect old sessions. Marks orphaned sessions that have been active t…
`getEnforcementMode()`	function	Get the current enforcement mode.
`isSessionEnforcementEnabled()`	function	Check if session enforcement is enabled.
`getActiveSessionInfo()`	function	Get active session info. Returns null if no active session.
`requireActiveSession()`	function	Require an active session for write operations. In strict mode, throws if no…
`validateTaskInScope()`	function	Validate that a task is within the current session’s scope. Only enforced whe…
`createAcceptanceEnforcement()`	function
`isValidPipelineStage()`	function	Check whether a string is a valid pipeline stage name.
`validatePipelineStage()`	function	Validate a pipeline stage name and throw a CleoError on failure.
`resolveDefaultPipelineStage()`	function	Determine the default pipeline stage for a new task. Rules (in priority orde…
`getPipelineStageOrder()`	function	Get the numeric order of a pipeline stage (1-based).
`isPipelineTransitionForward()`	function	Check whether transitioning from `currentStage` to `newStage` is forward-only…
`validatePipelineTransition()`	function	Validate a pipeline stage transition and throw if it would move backward.
`getLifecycleMode()`	function	Read `lifecycle.mode` from config. Falls back to “strict” when unset (matche…
`validateEpicCreation()`	function	Validate that a new epic satisfies creation requirements. In strict mode…
`validateChildStageCeiling()`	function	Validate that a child task’s pipeline stage does not exceed its epic’s stage…
`findEpicAncestor()`	function	Find the nearest epic ancestor for a given task. Walks the ancestor chain (r…
`validateEpicStageAdvancement()`	function	Validate that an epic can advance its pipeline stage. An epic is blocked…
`buildDefaultVerification()`	function	Build the default verification metadata applied to every new task. Gates are…
`validateTitle()`	function	Validate a task title. T4460
`validateStatus()`	function	Validate task status. T4460
`normalizePriority()`	function	Normalize priority to canonical string format. Accepts both string names (“cr…
`validatePriority()`	function	Validate task priority. T4460 T4572
`validateTaskType()`	function	Validate task type. T4460
`validateSize()`	function	Validate task size. T4460
`validateLabels()`	function	Validate label format. T4460
`validatePhaseFormat()`	function	Validate phase slug format. T4460
`validateDepends()`	function	Validate dependency IDs exist. T4460
`validateParent()`	function	Validate parent hierarchy constraints. T4460
`getTaskDepth()`	function	Get the depth of a task in the hierarchy. T4460
`inferTaskType()`	function	Infer task type from parent context. T4460
`getNextPosition()`	function	Get the next position for a task within a parent scope. T4460
`logOperation()`	function	Log an operation to the audit log. T4460
`findRecentDuplicate()`	function	Check for recent duplicate task. T4460
`addTask()`	function	Add a new task to the todo file. T4460
`listPhases()`	function	List all phases with status summaries. T4464
`showPhase()`	function	Show the current phase details. T4464
`setPhase()`	function	Set the current project phase. T4464
`startPhase()`	function	Start a phase (pending - active). T4464
`completePhase()`	function	Complete a phase (active - completed). T4464
`advancePhase()`	function	Advance to the next phase. T4464
`renamePhase()`	function	Rename a phase and update all task references. T4464
`deletePhase()`	function	Delete a phase with optional task reassignment. T4464
`pruneAuditLog()`	function	Prune old audit_log rows from tasks.db. 1. If auditRetentionDays is 0 or und…
`generateProjectHash()`	function	Canonical project identity hash. SHA-256 of absolute path, first 12 hex chars…
`validateAgainstSchema()`	function	Validate data against a JSON Schema object. Throws CleoError on validation fa…
`validateAgainstSchemaFile()`	function	Load a JSON Schema file and validate data against it.
`checkSchema()`	function	Check if data is valid against a schema without throwing. Returns an array of…
`resolveSchemaPath()`	function	Resolve the absolute path to a schema file at runtime. Priority: 1. Global…
`getSchemaVersion()`	function	Read the schema version from a resolved schema file. Checks `schemaVersion`…
`ensureGlobalSchemas()`	function	Copy ALL bundled schemas from package schemas/ to ~/.cleo/schemas/. - Create…
`checkGlobalSchemas()`	function	Verify that global schemas are installed and not stale.
`checkSchemaStaleness()`	function	Compare global schema versions against bundled package versions.
`listInstalledSchemas()`	function	List all schemas installed in ~/.cleo/schemas/.
`cleanProjectSchemas()`	function	Backup and remove deprecated .cleo/schemas/ directory from a project. Schema…
`readSchemaVersionFromFile()`	function	Read the top-level `schemaVersion` field from a schema file. Delegates to the…
`checkSchemaIntegrity()`	function	Check integrity of all active JSON files in a CLEO project.
`detectProjectType()`	function	Detect project type from directory contents. Returns a schema-compliant Proje…
`getInjectionTemplateContent()`	function	Get the CLEO-INJECTION.md template content from the package templates/ direct…
`ensureInjection()`	function	Full injection refresh: strip legacy blocks, inject CAAMP content, install gl…
`buildContributorInjectionBlock()`	function	Build a smart, contextual contributor block for AGENTS.md injection. Returns…
`checkInjection()`	function	Verify injection health: AGENTS.md exists, has CAAMP markers, markers are bal…
`fileExists()`	function	Check if a file exists and is readable.
`stripCLEOBlocks()`	function	Strip legacy CLEO:START/CLEO:END blocks from a file. Called before CAAMP inje…
`removeCleoFromRootGitignore()`	function	Remove .cleo/ or .cleo entries from the project root .gitignore.
`getPackageRoot()`	function	Resolve the package root directory (where schemas/ and templates/ live). scaf…
`getGitignoreContent()`	function	Load the gitignore template from the package’s templates/ directory. Falls ba…
`getCleoVersion()`	function	Read CLEO version from package.json.
`createDefaultConfig()`	function	Create default config.json content.
`ensureCleoStructure()`	function	Create .cleo/ directory and all required subdirectories. Idempotent: skips di…
`ensureGitignore()`	function	Create or repair .cleo/.gitignore from template. Idempotent: skips if file al…
`ensureConfig()`	function	Create default config.json if missing. Idempotent: skips if file already exists.
`ensureProjectInfo()`	function	Create or refresh project-info.json. Idempotent: skips if file already exists…
`ensureContributorMcp()`	function	No-op. Kept for API compatibility.
`ensureProjectContext()`	function	Detect and write project-context.json. Idempotent: skips if file exists and i…
`ensureCleoGitRepo()`	function	Initialize isolated .cleo/.git checkpoint repository. Idempotent: skips if .c…
`ensureSqliteDb()`	function	Create SQLite database if missing. Idempotent: skips if tasks.db already exists.
`checkCleoStructure()`	function	Verify all required .cleo/ subdirectories exist.
`checkGitignore()`	function	Verify .cleo/.gitignore exists and matches template.
`checkConfig()`	function	Verify config.json exists and is valid JSON.
`checkProjectInfo()`	function	Verify project-info.json exists with required fields.
`checkProjectContext()`	function	Verify project-context.json exists and is not stale (default: 30 days).
`checkCleoGitRepo()`	function	Verify .cleo/.git checkpoint repository exists.
`checkSqliteDb()`	function	Verify .cleo/tasks.db exists and is non-empty.
`ensureBrainDb()`	function	Create brain.db if missing. Idempotent: skips if brain.db already exists.
`checkBrainDb()`	function	Verify .cleo/brain.db exists and is non-empty.
`checkMemoryBridge()`	function	Verify .cleo/memory-bridge.md exists. Warning level if missing (not failure)…
`ensureGlobalHome()`	function	Ensure the global ~/.cleo/ home directory and its required subdirectories exi…
`ensureGlobalTemplates()`	function	Ensure the global CLEO injection template is installed. Delegates to injectio…
`ensureGlobalScaffold()`	function	Perform a complete global scaffold operation: ensure home and templates are a…
`ensureCleoOsHub()`	function	Ensure the CleoOS Hub subdirectories exist under the global CLEO home, and se…
`checkGlobalHome()`	function	Check that the global ~/.cleo/ home and its required subdirectories exist. Re…
`checkGlobalTemplates()`	function	Check that the global injection template is present and current. Read-only: n…
`checkLogDir()`	function	Check that the project log directory exists. Read-only: no side effects.
`classifyProject()`	function	Classify a project directory as greenfield or brownfield. Read-only — never…
`ensureGitHooks()`	function	Install or update managed git hooks from templates/git-hooks/ into .git/hooks…
`checkGitHooks()`	function	Verify managed hooks are installed and current. Compares installed hooks in…
`detectLegacyAgentOutputs()`	function	Detect legacy agent-output directories in a project. Read-only check — never…
`migrateAgentOutputs()`	function	Run the full agent-outputs migration. Copies files from all legacy locations…
`migrateJsonToSqlite()`	function	Migrate projects from legacy JSON registry to nexus.db. For each project ent…
`getNexusHome()`	function	Get path to the NEXUS home directory (cache, etc.).
`getNexusCacheDir()`	function	Get path to the NEXUS cache directory.
`getRegistryPath()`	function	Get path to the legacy projects registry JSON file.
`readRegistry()`	function	Read all projects from nexus.db and return as a NexusRegistryFile. Compatibil…
`readRegistryRequired()`	function	Read the global registry, throwing if not initialized.
`nexusInit()`	function	Initialize the NEXUS directory structure and nexus.db. Idempotent — safe to…
`nexusRegister()`	function	Register a project in the global registry (nexus.db).
`nexusUnregister()`	function	Unregister a project from the global registry.
`nexusList()`	function	List all registered projects.
`nexusGetProject()`	function	Get a project by name or hash. Returns null if not found.
`nexusProjectExists()`	function	Check if a project exists in the registry.
`nexusSync()`	function	Sync project metadata (task count, labels) for a registered project.
`nexusSyncAll()`	function	Sync all registered projects.
`nexusSetPermission()`	function	Update a project’s permission level in the registry. Used by permissions.ts t…
`nexusReconcile()`	function	Reconcile the current project’s identity with the global nexus registry. 4-s…
`analyzeStack()`	function
`analyzeArchitecture()`	function
`analyzeStructure()`	function
`analyzeConventions()`	function
`analyzeTesting()`	function
`analyzeIntegrations()`	function
`analyzeConcerns()`	function
`storeMapToBrain()`	function
`mapCodebase()`	function
`initAgentDefinition()`	function	Install cleo-subagent agent definition to ~/.agents/agents/. T4685
`initMcpServer()`	function	No-op. Kept for API compatibility. T4706
`initCoreSkills()`	function	Install CLEO core skills to the canonical skills directory via CAAMP. T4707…
`initNexusRegistration()`	function	Register/reconcile project with NEXUS. Uses nexusReconcile for idempotent han…
`installGitHubTemplates()`	function	Install GitHub issue and PR templates to .github/ if a git repo exists but .g…
`updateDocs()`	function	Run update-docs only: refresh all injections without reinitializing. Re-injec…
`initProject()`	function	Run full project initialization. Creates the .cleo/ directory structure, ins…
`isAutoInitEnabled()`	function	Check if auto-init is enabled via environment variable. T4789
`ensureInitialized()`	function	Check if a project is initialized and auto-init if configured. Returns initi…
`getVersion()`	function	Get the current CLEO/project version. Checks VERSION file, then package.json…
`bootstrapGlobalCleo()`	function	Bootstrap the global CLEO directory structure and install templates. Creates…
`installMcpToProviders()`	function	No-op. Kept for API compatibility.
`installSkillsGlobally()`	function	Install CLEO core skills globally via CAAMP.
`bootstrapCaamp()`	function
`exportTasks()`	function	Export tasks to a portable format. Returns the formatted content and metadata.
`importTasks()`	function	Import tasks from an export file.
`recordAgentExecution()`	function	Record an agent execution event to brain_decisions. Each event becomes a…
`_recordAgentExecutionWithAccessor()`	function	Internal implementation that accepts a pre-constructed accessor. Separated fo…
`getAgentPerformanceHistory()`	function	Retrieve agent execution performance history from brain_decisions. Queries a…
`_getAgentPerformanceHistoryWithAccessor()`	function	Internal implementation with injected accessor for testability.
`recordFailurePattern()`	function	Record a task failure pattern to brain_patterns. When a task fails, the (age…
`_recordFailurePatternWithAccessor()`	function	Internal implementation with injected accessor.
`storeHealingStrategy()`	function	Store a healing strategy observation to brain_observations. When a failure p…
`_storeHealingStrategyWithAccessor()`	function	Internal implementation with injected accessor.
`getSelfHealingSuggestions()`	function	Get self-healing suggestions for a given agent type and task type. Queries b…
`_getSelfHealingSuggestionsWithAccessor()`	function	Internal implementation with injected accessor.
`processAgentLifecycleEvent()`	function	Full agent lifecycle event processor. Convenience function that: 1. Records…
`getAgentCapacity()`	function	Get task-count-based remaining capacity for an agent. Remaining capacity =…
`getAgentsByCapacity()`	function	List all non-terminal agents sorted by remaining task capacity (descending)…
`getAgentSpecializations()`	function	Get the specialization/skills list for an agent. Specializations are stored…
`updateAgentSpecializations()`	function	Update the specializations list stored in an agent’s metadata. Merges the ne…
`recordAgentPerformance()`	function	Record agent performance metrics to the BRAIN execution history. Translates…
`updateCapacity()`	function	Update the capacity value for an agent instance.
`getAvailableCapacity()`	function	Get the total available capacity across all active agents. Only considers ag…
`findLeastLoadedAgent()`	function	Find the agent with the most available capacity.
`isOverloaded()`	function	Check if the system is overloaded (total capacity below threshold).
`getCapacitySummary()`	function	Get a capacity summary across the entire agent pool.
`recordHeartbeat()`	function	Record a heartbeat for an agent instance. Updates `last_heartbeat` to the cu…
`checkAgentHealth()`	function	Check the health of a specific agent instance by ID. Queries the agent’s cur…
`detectStaleAgents()`	function	Find all non-terminal agents whose last heartbeat is older than `thresholdMs`…
`detectCrashedAgents()`	function	Find agents with status `active` whose heartbeat has been silent for longer t…
`createRetryPolicy()`	function	Create a retry policy by merging overrides with the default policy.
`calculateDelay()`	function	Calculate the delay for a given retry attempt using exponential backoff.
`shouldRetry()`	function	Determine whether an error should be retried based on its classification and…
`withRetry()`	function	Wrap an async function with retry logic using configurable exponential backoff.
`recoverCrashedAgents()`	function	Attempt to recover crashed agents. Finds all agents with status ‘crashed’ an…
`calculateTaskRisk()`	function	Calculate the risk score for a task based on multiple contributing factors…
`predictValidationOutcome()`	function	Predict the likelihood of a task passing a lifecycle validation gate. Combin…
`gatherLearningContext()`	function	Gather applicable learnings for a task from brain_learnings.
`suggestGateFocus()`	function	Suggest which verification gates to focus on for a task, ordered by risk. Us…
`scoreVerificationConfidence()`	function	Compute a confidence score for a completed verification round and persist it…
`storePrediction()`	function	Store a validation prediction as a brain observation for future learning. Sa…
`predictAndStore()`	function	Compute a prediction for a task and immediately persist it to brain. Conveni…
`detectCircularDeps()`	function	Detect circular dependencies using DFS. Returns the cycle path if found, empt…
`wouldCreateCycle()`	function	Check if adding a dependency would create a cycle.
`getBlockedTasks()`	function	Get tasks that are blocked (have unmet dependencies).
`getReadyTasks()`	function	Get tasks that are ready (all dependencies met).
`getDependents()`	function	Get tasks that depend on a given task.
`getDependentIds()`	function	Get dependent IDs.
`getUnresolvedDeps()`	function	Get unresolved dependencies for a task (deps that are not done/cancelled).
`validateDependencyRefs()`	function	Validate dependencies for missing references.
`validateDependencies()`	function	Full dependency graph validation.
`topologicalSort()`	function	Topological sort of tasks by dependencies. Returns sorted task IDs or null if…
`getTransitiveBlockers()`	function	Walk upstream recursively through a task’s dependency chain. Returns all non-…
`getLeafBlockers()`	function	From the transitive blockers, return only “leaf” blockers — those whose own d…
`computeDependencyWaves()`	function	Compute dependency waves for parallel execution. Tasks in the same wave can r…
`getNextTask()`	function	Get the next task to work on (highest priority ready task).
`getCriticalPath()`	function	Calculate the critical path (longest dependency chain). Returns task IDs alon…
`getTaskOrder()`	function	Get task ordering by dependency + priority.
`getParallelTasks()`	function	Get parallelizable tasks (tasks with no unmet dependencies).
`analyzeTaskImpact()`	function	Analyze the full downstream impact of a task. Computes direct and transitive…
`analyzeChangeImpact()`	function	Analyze the downstream effects of a specific change to a task. Predicts what…
`calculateBlastRadius()`	function	Calculate the blast radius for a task. Quantifies how many tasks, epics, and…
`predictImpact()`	function	Predict the downstream impact of a free-text change description. Uses fuzzy…
`extractPatternsFromHistory()`	function	Analyze brain_observations and task history to find recurring patterns. Dete…
`matchPatterns()`	function	Find which known patterns from brain_patterns apply to a given task. Compare…
`storeDetectedPattern()`	function	Save a detected pattern to the brain_patterns table. Uses the existing brain…
`updatePatternStats()`	function	Update the frequency and success_rate of an existing pattern after an outcome…
`validateSyntax()`	function	Validate a query string matches expected syntax.
`parseQuery()`	function	Parse a query string into its components.
`getCurrentProject()`	function	Get the current project name from context. Reads .cleo/project-info.json or f…
`resolveProjectPath()`	function	Resolve a project name to its filesystem path. Handles special cases: ”.” (cu…
`resolveTask()`	function	Resolve a query to task data. For wildcard queries, returns an array of match…
`getProjectFromQuery()`	function	Extract the project name from a query without full resolution. Useful for per…
`extractKeywords()`	function	Extract meaningful keywords from text (filters stop words and short tokens).
`discoverRelated()`	function	Discover tasks related to a given task query across projects. Returns a stru…
`searchAcrossProjects()`	function	Search for tasks across all registered projects. Returns a structured result…
`permissionLevel()`	function	Convert a permission string to its numeric level. Returns 0 for invalid/unkno…
`getPermission()`	function	Get the permission level for a registered project. Returns ‘read’ as default…
`checkPermission()`	function	Check if a project has sufficient permissions (non-throwing). Uses hierarchic…
`requirePermission()`	function	Require a permission level or throw CleoError. Used as a guard at the start o…
`checkPermissionDetail()`	function	Full permission check returning a structured result.
`setPermission()`	function	Set the permission level for a project. Validates the permission value and up…
`canRead()`	function	Convenience: check read access.
`canWrite()`	function	Convenience: check write access.
`canExecute()`	function	Convenience: check execute access.
`matchesPattern()`	function	Match a file path against a glob-like pattern. Supports: ’*’ (single segment…
`getSharingStatus()`	function	Get the sharing status: which .cleo/ files are tracked vs ignored, plus git s…
`syncGitignore()`	function	Sync the project .gitignore to match the sharing config. Adds/updates a manag…
`currentTask()`	function	Show current task work state. T4462 T4750
`startTask()`	function	Start working on a specific task. T4462 T4750
`stopTask()`	function	Stop working on the current task. T4462 T4750
`getWorkHistory()`	function	Get task work history from session notes. T4462 T4750
`completeTask()`	function	Complete a task by ID. Handles dependency checking and optional auto-completi…
`validateTitleDescription()`	function	Validate that title and description are both present and different. This is a…
`validateTimestamps()`	function	Validate that timestamps are not in the future
`validateIdUniqueness()`	function	Validate ID uniqueness across all tasks (todo + archive)
`validateNoDuplicateDescription()`	function	Validate no duplicate task descriptions
`validateHierarchy()`	function	Validate hierarchy constraints. Accepts optional limits to override defaults…
`validateStatusTransition()`	function	Validate status transition
`validateNewTask()`	function	Run all validation rules on a task being created
`hasErrors()`	function	Check if violations contain any errors (not just warnings)
`updateTask()`	function	Update a task’s fields. T4461
`parseDirective()`	function	Parse a Conduit message into a structured directive. Extracts directive verb…
`routeDirective()`	function	Route a Conduit directive to the correct project’s CLEO instance. Resolves w…
`workspaceStatus()`	function	Get aggregated task status across all registered projects. Returns per-proje…
`workspaceAgents()`	function	Get all agents registered across all projects. Queries each project’s agent_…
`invalidateDepsCache()`	function	Invalidate the cached TaskFile (call after writes). T4659 T4654
`buildGraph()`	function	Build an adjacency graph from task dependencies. T4464
`getDepsOverview()`	function	Get dependency overview for all tasks. T4464
`getTaskDeps()`	function	Get dependencies for a specific task. T4464
`topologicalSort()`	function	Topological sort of tasks respecting dependencies. Returns tasks in execution…
`getExecutionWaves()`	function	Group tasks into parallelizable execution waves. T4464
`getCriticalPath()`	function	Find the critical path (longest dependency chain) from a task. T4464
`getImpact()`	function	Find all tasks affected by changes to a given task. T4464
`detectCycles()`	function	Detect circular dependencies in the task graph. T4464
`getTaskTree()`	function	Build task hierarchy tree. T4464
`addRelation()`	function	Manage task relationships (relates/blocks). T4464
`buildDependencyGraph()`	function	Build a dependency graph for a set of tasks. Returns a Map from task ID to t…
`detectCircularDependencies()`	function	Detect circular dependencies using DFS traversal.
`findMissingDependencies()`	function	Find missing dependencies — deps that reference tasks outside the epic that a…
`analyzeDependencies()`	function	Perform full dependency analysis for an epic’s children. Combines dependency…
`countManifestEntries()`	function	Count manifest entries from pipeline_manifest (ADR-027).
`estimateContext()`	function	Estimate context usage for orchestration.
`OrchestrationHierarchyImpl`	class	Concrete implementation of OrchestrationHierarchyAPI.
`computeWaves()`	function	Compute execution waves using topological sort.
`getEnrichedWaves()`	function	Get enriched wave data for an epic.
`countByStatus()`	function	Count tasks by status.
`computeEpicStatus()`	function	Compute epic-specific status.
`computeOverallStatus()`	function	Compute overall orchestration status across all tasks.
`computeProgress()`	function	Compute progress metrics for all tasks.
`computeStartupSummary()`	function	Compute startup summary for an epic.
`startOrchestration()`	function	Start an orchestrator session for an epic. T4466
`analyzeEpic()`	function	Analyze an epic’s dependency structure. T4466
`getReadyTasks()`	function	Get parallel-safe ready tasks for an epic. T4466
`getNextTask()`	function	Get the next task to work on for an epic. T4466
`prepareSpawn()`	function	Prepare a spawn context for a subagent. T4466
`validateSpawnOutput()`	function	Validate a subagent’s output. T4466
`getOrchestratorContext()`	function	Get orchestrator context summary. T4466
`autoDispatch()`	function	Auto-dispatch: determine the protocol for a task based on metadata. T4466
`resolveTokens()`	function	Resolve tokens in a prompt string. T4466
`getLinksByProvider()`	function	Find all links for a given provider.
`getLinkByExternalId()`	function	Find a link by provider + external ID.
`getLinksByTaskId()`	function	Find all links for a given CLEO task.
`createLink()`	function	Create a new external task link.
`touchLink()`	function	Update the lastSyncAt and optionally the title/metadata for an existing link.
`removeLinksByProvider()`	function	Remove all links for a provider (used during provider deregistration).
`reconcile()`	function	Reconcile external task state with CLEO’s authoritative task store.
`getArtifactHandler()`	function	Get handler for an artifact type. T4552
`hasArtifactHandler()`	function	Check if a handler is registered for an artifact type. T4552
`buildArtifact()`	function	Build an artifact using the appropriate handler. T4552
`validateArtifact()`	function	Validate an artifact using the appropriate handler. T4552
`publishArtifact()`	function	Publish an artifact using the appropriate handler. T4552
`getSupportedArtifactTypes()`	function	Get all supported artifact types. T4552
`parseChangelogBlocks()`	function	Parse [custom-log]…[/custom-log] blocks from a CHANGELOG section. Returns t…
`writeChangelogSection()`	function	Write or update a CHANGELOG.md section for a specific version. - If ## [VERS…
`loadReleaseConfig()`	function	Load release configuration with defaults.
`validateReleaseConfig()`	function	Validate release configuration.
`getArtifactType()`	function	Get artifact type from config.
`getReleaseGates()`	function	Get release gates from config.
`getChangelogConfig()`	function	Get changelog configuration.
`getDefaultGitFlowConfig()`	function	Return the default GitFlow branch configuration.
`getGitFlowConfig()`	function	Merge caller-supplied GitFlow config with defaults.
`getDefaultChannelConfig()`	function	Return the default channel configuration.
`getChannelConfig()`	function	Merge caller-supplied channel config with defaults.
`getPushMode()`	function	Return the configured push mode, defaulting to ‘auto’.
`getDefaultChannelConfig()`	function	Return the default branch-to-channel mapping.
`resolveChannelFromBranch()`	function	Resolve the release channel for a given Git branch name. Resolution order: 1…
`channelToDistTag()`	function	Map a release channel to its npm dist-tag string. Kept as an explicit functi…
`validateVersionChannel()`	function	Validate that a version string satisfies the pre-release conventions for the…
`describeChannel()`	function	Return a human-readable description of the given release channel.
`getPlatformPath()`	function	Get the output path for a CI platform.
`detectCIPlatform()`	function	Detect the CI platform from the project.
`generateCIConfig()`	function	Generate CI config for a platform.
`writeCIConfig()`	function	Write CI config to the appropriate path.
`validateCIConfig()`	function	Validate an existing CI config.
`isGhCliAvailable()`	function	Check if the `gh` CLI is available by attempting to run `gh --version`. Does…
`extractRepoOwnerAndName()`	function	Parse a GitHub remote URL (HTTPS or SSH) into owner and repo components. Retu…
`detectBranchProtection()`	function	Detect whether a branch has protection rules enabled. Strategy 1 (preferred)…
`buildPRBody()`	function	Build the markdown body for a GitHub pull request.
`formatManualPRInstructions()`	function	Format human-readable instructions for creating a PR manually.
`createPullRequest()`	function	Create a GitHub pull request using the `gh` CLI, or return manual instruction…
`checkEpicCompleteness()`	function	Check epic completeness for a set of release task IDs. Verifies all children…
`checkDoubleListing()`	function	Check if any tasks are listed in multiple releases.
`validateVersionFormat()`	function	Validate version format (semver X.Y.Z or CalVer YYYY.M.patch, with optional p…
`isCalVer()`	function	Check if a version string is CalVer format.
`calculateNewVersion()`	function	Calculate new version from current + bump type.
`getVersionBumpConfig()`	function	Get version bump configuration, mapping config field names to VersionBumpTarget.
`isVersionBumpConfigured()`	function	Check if version bump is configured.
`bumpVersionFromConfig()`	function	Bump version in all configured files.
`prepareRelease()`	function	Prepare a release (create a release manifest entry). T4788
`generateReleaseChangelog()`	function	Generate changelog for a release. T4788
`listManifestReleases()`	function	List all releases. T4788
`showManifestRelease()`	function	Show release details. T4788
`commitRelease()`	function	Mark release as committed (metadata only). T4788
`tagRelease()`	function	Mark release as tagged (metadata only). T4788
`runReleaseGates()`	function	Run release validation gates. T4788 T5586
`cancelRelease()`	function	Cancel and remove a release in draft or prepared state. Only releases that ha…
`rollbackRelease()`	function	Rollback a release. T4788
`pushRelease()`	function	Push release to remote via git. Respects config.release.push policy: - remot…
`markReleasePushed()`	function	Update release status after push, with optional provenance fields. T4788 T5580
`migrateReleasesJsonToSqlite()`	function	One-time migration: read .cleo/releases.json and insert each release into the…
`serializeSession()`	function	Serialize a session into a complete snapshot. Captures the full session stat…
`restoreSession()`	function	Restore a session from a snapshot. Hydrates a session from a previously seri…
`archiveSticky()`	function	Archive a sticky note.
`convertStickyToTask()`	function	Convert a sticky note to a task.
`convertStickyToMemory()`	function	Convert a sticky note to a memory observation.
`convertStickyToTaskNote()`	function	Convert a sticky note to a task note.
`convertStickyToSessionNote()`	function	Convert a sticky note to a session note.
`generateStickyId()`	function	Generate the next sticky note ID. Finds the highest existing SN-XXX ID and i…
`addSticky()`	function	Create a new sticky note.
`listStickies()`	function	List sticky notes with optional filters.
`purgeSticky()`	function	Purge (permanently delete) a sticky note.
`getSticky()`	function	Get a sticky note by ID.
`archiveTasks()`	function	Archive completed (and optionally cancelled) tasks. Moves them from active ta…
`deleteTask()`	function	Delete a task (soft delete - moves to archive). T4461
`Cleo`	class
`calculateExportChecksum()`	function	Calculate SHA-256 checksum for export integrity (truncated to 16 hex chars).
`verifyExportChecksum()`	function	Verify export package checksum.
`buildIdMap()`	function	Build ID map from tasks.
`buildRelationshipGraph()`	function	Build relationship graph from tasks.
`buildExportPackage()`	function	Build a complete export package.
`exportSingle()`	function	Export a single task.
`exportSubtree()`	function	Export a subtree (task + all descendants).
`exportTasksPackage()`	function	Export tasks to a portable cross-project package.
`getCostHint()`	function	Determine cost hint for an operation based on domain and operation name.
`groupOperationsByDomain()`	function	Group operations by domain into a compact format.
`buildVerboseOperations()`	function	Build verbose operation entries with cost hints.
`computeHelp()`	function	Compute the help result for the admin.help operation. Accepts the full OPERA…
`getNextAvailableId()`	function	Get the next available task ID number from existing tasks.
`generateRemapTable()`	function	Generate a remap table for importing tasks. Maps source task IDs to new seque…
`validateRemapTable()`	function	Validate that a remap table is complete and consistent.
`remapTaskId()`	function	Remap a single task ID, returning original if not in table.
`remapTaskReferences()`	function	Remap all ID references in a task.
`detectDuplicateTitles()`	function	Detect duplicate titles between import and target.
`resolveDuplicateTitle()`	function	Resolve duplicate title by appending suffix.
`importFromPackage()`	function	Import tasks from an in-memory ExportPackage with ID remapping. Core logic ex…
`importTasksPackage()`	function	Import tasks from a cross-project export package file with ID remapping. Thin…
`findAdrs()`	function
`listAdrs()`	function	List ADRs from .cleo/adrs/ directory with optional status filter
`showAdr()`	function	Retrieve a single ADR by ID (e.g., ‘ADR-007’)
`validateAllAdrs()`	function	Validate all ADRs in .cleo/adrs/ against the schema
`providerList()`	function	List all registered providers. T4332
`providerGet()`	function	Get a single provider by ID or alias. T4332
`providerDetect()`	function	Detect all providers installed on the system. T4332
`providerInstalled()`	function	Get providers that are installed on the system. T4332
`providerCount()`	function	Get count of registered providers. T4332
`registryVersion()`	function	Get CAAMP registry version. T4332
`injectionCheck()`	function	Check injection status for a single file. T4332
`injectionCheckAll()`	function	Check injection status across all providers. T4332
`injectionUpdate()`	function	Inject or update content in a single file. T4332
`injectionUpdateAll()`	function	Inject content to all providers’ instruction files. T4332
`batchInstallWithRollback()`	function	Install multiple skills atomically with rollback on failure. T4705 T4663
`checkProviderCapability()`	function	Check if provider supports a specific capability
`checkProviderCapabilities()`	function	Check multiple capabilities at once
`detectLanguage()`	function	Detect tree-sitter language from a file path.
`grammarPackage()`	function	Get the npm grammar package name for a language.
`isTreeSitterAvailable()`	function	Check if tree-sitter CLI is available and executable. Cached after first call.
`parseFile()`	function	Parse a single file and extract code symbols.
`batchParse()`	function	Batch-parse multiple files, grouping by language for efficiency. Files with…
`smartOutline()`	function	Generate a smart outline for a source file. Returns a tree of symbols with s…
`smartSearch()`	function	Search for symbols across a codebase. Walks the directory tree, batch-parses…
`smartUnfold()`	function	Extract a symbol’s complete source from a file. Finds the symbol by name (su…
`getComplianceJsonlPath()`	function	Resolve COMPLIANCE.jsonl path for a project root.
`readComplianceJsonl()`	function	Read COMPLIANCE.jsonl entries. Invalid JSON lines are skipped to preserve app…
`appendComplianceJsonl()`	function	Append one entry to COMPLIANCE.jsonl, creating directories as needed.
`getComplianceSummary()`	function	Get compliance summary.
`listComplianceViolations()`	function	List compliance violations.
`getComplianceTrend()`	function	Get compliance trend.
`auditEpicCompliance()`	function	Audit epic compliance.
`syncComplianceMetrics()`	function	Sync compliance metrics to a summary file.
`getSkillReliability()`	function	Get skill reliability stats.
`getValueMetrics()`	function	Get value metrics (T2833).
`ConduitClient`	class	ConduitClient wraps a Transport, adding high-level messaging semantics.
`HttpTransport`	class	HTTP transport with automatic primary/fallback failover.
`LocalTransport`	class	In-process SQLite transport for fully offline agent messaging.
`SseTransport`	class	SseTransport — real-time SSE with HTTP polling fallback.
`resolveTransport()`	function	Resolve the best available transport for a credential. Cloud-backed agents (…
`createConduit()`	function	Create a Conduit instance from the agent registry.
`getContextStatus()`	function	Get context status.
`checkContextThreshold()`	function	Check context threshold (returns exit code info).
`listContextSessions()`	function	List all context state files.
`validatePayload()`	function	Validate a hook payload against its event-specific Zod schema. Falls back to…
`injectTasks()`	function	Inject tasks for external consumption.
`collectDiagnostics()`	function	Collect system diagnostics for bug reports.
`formatDiagnosticsTable()`	function	Format diagnostics as markdown table.
`parseIssueTemplates()`	function	Parse all issue templates from available sources. Priority: 1. Packaged tem…
`getTemplateConfig()`	function	Get template configuration - tries live parse, cache, then fallback.
`getTemplateForSubcommand()`	function	Get the template for a specific subcommand (bug, feature, etc.).
`cacheTemplates()`	function	Cache parsed templates to .cleo/issue-templates.json.
`validateLabelsExist()`	function	Validate that labels referenced in issue templates are consistent. Collects…
`buildIssueBody()`	function	Build structured issue body with template sections.
`checkGhCli()`	function	Check that gh CLI is installed and authenticated.
`addIssue()`	function	Add a GitHub issue for a given type (bug, feature, help). Returns structured…
`withRetry()`	function	Execute an async function with automatic retry and exponential backoff.
`computeDelay()`	function	Compute the wait time before the next attempt.
`applyTemporalDecay()`	function	Apply temporal decay to brain_learnings confidence values. Entries older tha…
`consolidateMemories()`	function	Consolidate old observations by keyword similarity. Groups observations olde…
`migrateBrainData()`	function	Migrate BRAIN memory data from JSONL files to brain.db. Reads: - .cleo/memor…
`addResearch()`	function	Add a research entry.
`showResearch()`	function	Show a specific research entry.
`listResearch()`	function	List research entries with optional filtering.
`pendingResearch()`	function	List pending research entries.
`linkResearch()`	function	Link a research entry to a task.
`updateResearch()`	function	Update research findings.
`statsResearch()`	function	Get research statistics.
`linksResearch()`	function	Get research entries linked to a specific task.
`archiveResearch()`	function	Archive old research entries by status. Moves ‘complete’ entries to an archiv…
`readManifest()`	function	Read manifest entries from the legacy agent-outputs flat-file (deprecated per ADR-027).
`appendManifest()`	function	Append a manifest entry.
`queryManifest()`	function	Query manifest entries with filtering.
`readExtendedManifest()`	function	Read all manifest entries as extended entries.
`filterManifestEntries()`	function	Filter manifest entries by criteria.
`showManifestEntry()`	function	Show a manifest entry by ID with optional file content.
`searchManifest()`	function	Search manifest entries by text with relevance scoring.
`pendingManifestEntries()`	function	Get pending manifest entries (partial, blocked, or needing followup).
`manifestStats()`	function	Get manifest-based research statistics.
`linkManifestEntry()`	function	Link a manifest entry to a task (adds taskId to linked_tasks array).
`appendExtendedManifest()`	function	Append an extended manifest entry. Validates required fields before appending.
`archiveManifestEntries()`	function	Archive manifest entries older than a date.
`findContradictions()`	function	Find manifest entries with overlapping topics but conflicting key_findings.
`findSuperseded()`	function	Identify research entries replaced by newer work on same topic.
`readProtocolInjection()`	function	Read protocol injection content for a given protocol type.
`compactManifest()`	function	Compact the legacy agent-outputs flat-file by removing duplicate/stale entries.
`validateManifestEntries()`	function	Validate research entries for a task.
`ensureMetricsDir()`	function	Ensure metrics directory exists, returning its path.
`getCompliancePath()`	function	Get compliance log path.
`getViolationsPath()`	function	Get violations log path.
`getSessionsMetricsPath()`	function	Get sessions metrics log path.
`isoTimestamp()`	function	Generate ISO 8601 UTC timestamp.
`isoDate()`	function	Generate ISO 8601 date only.
`readJsonlFile()`	function	Read a JSONL file into an array of parsed objects.
`getComplianceSummaryBase()`	function	Get compliance summary from log file.
`isOtelEnabled()`	function	Check if OTel telemetry is enabled.
`getOtelSetupCommands()`	function	Get environment variable commands for OTel capture setup.
`parseTokenMetrics()`	function	Parse OTel token metrics from collected data.
`getSessionTokens()`	function	Get aggregated token counts from OTel data.
`recordSessionStart()`	function	Record token counts at session start.
`recordSessionEnd()`	function	Record token counts at session end.
`compareSessions()`	function	Compare token usage between two sessions.
`getTokenStats()`	function	Get statistics about token usage across sessions.
`logABEvent()`	function	Log an A/B test event.
`startABTest()`	function	Start an A/B test session.
`endABTest()`	function	End an A/B test session with summary.
`getABTestResults()`	function	Get results for a specific test variant.
`listABTests()`	function	List all A/B tests.
`compareABTest()`	function	Compare two variants of the same test.
`getABTestStats()`	function	Get aggregate statistics of all A/B tests.
`syncMetricsToGlobal()`	function	Sync project metrics to global aggregation file.
`getProjectComplianceSummary()`	function	Get compliance summary for the current project.
`getGlobalComplianceSummary()`	function	Get compliance summary across all projects.
`getComplianceTrend()`	function	Get compliance trend over time.
`getSkillReliability()`	function	Get reliability stats per skill/agent.
`logSessionMetrics()`	function	Log session metrics to SESSIONS.jsonl.
`getSessionMetricsSummary()`	function	Get summary of session metrics.
`isValidEnumValue()`	function	Validate that a value is a member of a given enum.
`estimateTokens()`	function	Estimate token count from text. ~4 characters per token.
`estimateTokensFromFile()`	function	Estimate token count from a file.
`logTokenEvent()`	function	Log a token usage event to the JSONL file.
`trackFileRead()`	function	Track a file read with token estimate.
`trackManifestQuery()`	function	Track a manifest query (partial read).
`trackSkillInjection()`	function	Track skill injection with tokens.
`trackPromptBuild()`	function	Track final prompt size.
`trackSpawnOutput()`	function	Track subagent output tokens.
`trackSpawnComplete()`	function	Track complete spawn cycle (prompt + output).
`startTokenSession()`	function	Start tracking tokens for a session.
`endTokenSession()`	function	End token tracking session with summary.
`getTokenSummary()`	function	Get token usage summary for a time period.
`compareManifestVsFull()`	function	Compare manifest vs full file token usage strategies.
`getTrackingStatus()`	function	Get tracking status.
`computeChecksum()`	function	Compute SHA-256 checksum of a file.
`verifyBackup()`	function	Verify that a backup file matches the source file and is a valid SQLite datab…
`compareChecksums()`	function	Quick checksum comparison without SQLite verification. Use when you only need…
`MigrationLogger`	class	Structured logger for migration operations
`createMigrationLogger()`	function	Create a migration logger for the given cleo directory. Convenience function…
`readMigrationLog()`	function	Read and parse a migration log file.
`logFileExists()`	function	Check if a log file exists and is readable.
`getLatestMigrationLog()`	function	Get the most recent migration log file for a cleo directory.
`checkStorageMigration()`	function	Check whether legacy JSON data needs to be migrated to SQLite. Returns a dia…
`createMigrationState()`	function	Create initial migration state at the start of migration. Captures source fi…
`updateMigrationState()`	function	Update migration state with partial updates. Merges updates with existing st…
`updateMigrationPhase()`	function	Update just the migration phase. Convenience wrapper for common phase transit…
`updateMigrationProgress()`	function	Update progress counters during import.
`addMigrationError()`	function	Add an error to the migration state.
`addMigrationWarning()`	function	Add a warning to the migration state.
`loadMigrationState()`	function	Load existing migration state.
`isMigrationInProgress()`	function	Check if a migration is in progress.
`canResumeMigration()`	function	Check if migration can be resumed.
`completeMigration()`	function	Mark migration as complete.
`failMigration()`	function	Mark migration as failed with error details.
`clearMigrationState()`	function	Clear migration state file. Safe to call even if state doesn’t exist.
`getMigrationSummary()`	function	Get a summary of migration state for display.
`verifySourceIntegrity()`	function	Verify source files haven’t changed since migration started. Compares curren…
`validateSourceFiles()`	function	Validate all JSON source files before migration. This function MUST be calle…
`formatValidationResult()`	function	Format validation result for human-readable output.
`checkTaskCountMismatch()`	function	Check for task count mismatch between existing database and JSON. This helps…
`detectVersion()`	function	Detect schema version from a data file. T4468
`compareSemver()`	function	Compare two version strings (X.Y.Z format, works for both semver and CalVer)…
`getMigrationStatus()`	function	Get migration status for all data files. T4468
`runMigration()`	function	Run migrations on a data file. T4468
`runAllMigrations()`	function	Run all pending migrations. T4468
`invalidateGraphCache()`	function	Invalidate the in-memory graph cache.
`buildGlobalGraph()`	function	Build the global dependency graph from all registered projects. Uses checksum…
`nexusDeps()`	function	Show dependencies for a task across projects. Supports forward (what this dep…
`resolveCrossDeps()`	function	Resolve an array of dependencies (local or cross-project).
`criticalPath()`	function	Calculate the critical path across project boundaries. Returns the longest de…
`blockingAnalysis()`	function	Analyze the blocking impact of a task across all projects. Uses BFS to find a…
`orphanDetection()`	function	Detect orphaned cross-project dependencies. Finds tasks with dependency refer…
`previewTransfer()`	function	Preview a transfer without writing any data. Validates projects, permissions,…
`executeTransfer()`	function	Execute a cross-project task transfer. Pipeline: 1. Validate source/target…
`compareLevels()`	function	Compare two pino levels numerically. Returns negative if a b, 0 if equal, po…
`matchesFilter()`	function	Check if a single entry matches the filter criteria. All specified fields mus…
`filterEntries()`	function	Filter an array of parsed log entries against criteria. Returns entries match…
`paginate()`	function	Apply pagination (limit/offset) to a result set.
`isValidLevel()`	function	Validate that a string is a valid PinoLevel.
`parseLogLine()`	function	Parse a single JSONL line into a PinoLogEntry. Returns null for empty lines,…
`parseLogLines()`	function	Parse multiple JSONL lines into PinoLogEntry array. Skips malformed lines.
`getProjectLogDir()`	function	Get the project log directory path. Uses getLogDir() from logger if available…
`getGlobalLogDir()`	function	Get the global log directory path (~/.cleo/logs/).
`discoverLogFiles()`	function	Discover all log files in the specified scope. Returns file info sorted by da…
`readLogFileLines()`	function	Read all lines from a log file synchronously. Returns raw JSON strings (one p…
`streamLogFileLines()`	function	Create an async iterable over lines of a log file. Suitable for large files -…
`queryLogs()`	function	High-level query: discover files, parse, filter, paginate. Convenience wrappe…
`streamLogs()`	function	Stream-based query for large log datasets. Yields matching entries one at a t…
`getLogSummary()`	function	Get a summary of log activity (counts by level, date range, subsystems). Read…
`getOtelStatus()`	function	Get token tracking status.
`getOtelSummary()`	function	Get combined token usage summary.
`getOtelSessions()`	function	Get session-level token data.
`getOtelSpawns()`	function	Get spawn-level token data.
`getRealTokenUsage()`	function	Get real token usage from Claude Code API.
`clearOtelData()`	function	Clear token tracking data with backup.
`listPhases()`	function	List all phases with status summaries. T5326
`showPhase()`	function	Show phase details by slug or current phase. T5326
`getCurrentBranch()`	function	Get the current branch name in .cleo/.git. T4884
`addRemote()`	function	Add a git remote to .cleo/.git. T4884
`removeRemote()`	function	Remove a git remote from .cleo/.git. T4884
`listRemotes()`	function	List configured remotes in .cleo/.git. T4884
`push()`	function	Push .cleo/.git to a remote. T4884
`pull()`	function	Pull from a remote into .cleo/.git. Uses rebase strategy to maintain clean hi…
`getSyncStatus()`	function	Get the sync status between local .cleo/.git and remote. T4884
`getRoadmap()`	function	Get roadmap from pending epics and CHANGELOG history.
`getOperationMode()`	function	Lookup the execution mode for a specific operation
`canRunNatively()`	function	Check if an operation can run natively (without CLI)
`requiresCLI()`	function	Check if an operation requires CLI
`getNativeOperations()`	function	Get all native-capable operations for a domain
`generateCapabilityReport()`	function	Generate a capability report for system.doctor
`getCapabilityMatrix()`	function	Get the full capability matrix (for testing/introspection)
`findHighestId()`	function	Find the highest existing task ID number
`generateNextIdFromSet()`	function	Generate the next ID given an explicit set of existing IDs. Useful when calle…
`isValidTaskId()`	function	Validate that a task ID matches the expected format
`normalizeTaskId()`	function	Normalize a task ID input to canonical T#### format. Accepts various loose f…
`SecurityError`	class	Security validation error thrown when input fails sanitization
`sanitizeTaskId()`	function	Sanitize and validate a task ID
`sanitizePath()`	function	Sanitize and validate a file path
`sanitizeContent()`	function	Sanitize content string
`validateEnum()`	function	Validate that a value is in an allowed enum set
`RateLimiter`	class	In-memory sliding window rate limiter
`ensureArray()`	function	Normalize a value to an array of strings. Handles external clients sending co…
`sanitizeParams()`	function	Sanitize all params in a request before routing
`getAgentsDir()`	function	Get the agents directory path. T4518
`parseAgentConfig()`	function	Parse an AGENT.md file into an AgentConfig. AGENT.md uses the same YAML front…
`loadAgentConfig()`	function	Load agent configuration by name. Searches in the agents/ directory. T4518
`getSubagentConfig()`	function	Get the cleo-subagent configuration (universal executor). T4518
`agentExists()`	function	Check if an agent definition exists. T4518
`installAgent()`	function	Install a single agent via symlink. T4518
`installAllAgents()`	function	Install all agents from the project agents/ directory. T4518
`uninstallAgent()`	function	Uninstall a single agent by removing its symlink. T4518
`getRegistryPath()`	function	Get the agent registry file path. T4518
`readRegistry()`	function	Read the agent registry, creating if needed. T4518
`saveRegistry()`	function	Save the agent registry. T4518
`registerAgent()`	function	Register an agent in the registry. T4518
`unregisterAgent()`	function	Unregister an agent from the registry. T4518
`getAgent()`	function	Get an agent from the registry by name. T4518
`listAgents()`	function	List all registered agents. T4518
`syncRegistry()`	function	Scan the agents/ directory and register all found agents. T4518
`loadProtocolBase()`	function	Load the subagent protocol base content. T4521
`buildTaskContext()`	function	Build task context block for injection into a subagent prompt. T4521
`filterProtocolByTier()`	function	Filter protocol content by MVI tier. Extracts sections based on !— TIER:X —…
`injectProtocol()`	function	Inject the subagent protocol into skill content. Composes: skill content + pr…
`orchestratorSpawnSkill()`	function	Full orchestrator spawn workflow (skill-based). High-level function that load…
`prepareTokenValues()`	function	Prepare standard token values for a task spawn. T4521
`installSkill()`	function	Install a single skill via CAAMP.
`generateContributionId()`	function	Generate a unique contribution ID. T4520
`validateContributionTask()`	function	Validate that a task is suitable for contribution protocol. T4520
`getContributionInjection()`	function	Generate the contribution injection block for a subagent prompt. T4520
`detectConflicts()`	function	Detect conflicts between two sets of decisions. T4520
`computeConsensus()`	function	Compute weighted consensus from multiple agent decisions. T4520
`createContributionManifestEntry()`	function	Create a manifest entry for a contribution. T4520
`ensureOutputs()`	function	Ensure agent outputs directory and manifest file exist. T4520
`readManifest()`	function	Read all manifest entries. T4520
`appendManifest()`	function	Append a manifest entry (atomic JSONL append). T4520
`findEntry()`	function	Find a manifest entry by ID. T4520
`filterEntries()`	function	Filter manifest entries by criteria. T4520
`getPendingFollowup()`	function	Get entries with pending follow-ups. T4520
`getFollowupTaskIds()`	function	Get unique follow-up task IDs from all manifest entries. T4520
`taskHasResearch()`	function	Check if a task has linked research. T4520
`archiveEntry()`	function	Archive a manifest entry (move to archive status). T4520
`rotateManifest()`	function	Rotate manifest by archiving old entries. T4520
`isCacheFresh()`	function	Check if the cached manifest is fresh (within TTL). T4520
`invalidateCache()`	function	Invalidate the cache (delete the cached manifest). T4520
`resolveManifest()`	function	Resolve the skills manifest. Returns a cached version if fresh, otherwise gen…
`regenerateCache()`	function	Force regenerate the cache. T4520
`loadConfig()`	function	Load SkillsMP configuration from skillsmp.json. T4521
`searchSkills()`	function	Search the skills marketplace. Delegates to CAAMP’s searchSkills for the actu…
`getSkill()`	function	Get a specific skill from the marketplace. Uses CAAMP’s MarketplaceClient for…
`isEnabled()`	function	Check if the marketplace is enabled and reachable. T4521
`buildPrompt()`	function	Build a fully-resolved prompt for spawning a subagent. T4519
`spawn()`	function	Generate full spawn command with metadata. T4519
`canParallelize()`	function	Check if tasks can be spawned in parallel (no inter-dependencies). T4519
`spawnBatch()`	function	Spawn prompts for multiple tasks in a batch. Ports orchestrator_spawn_batch f…
`getThresholds()`	function	Get orchestrator context thresholds from config or defaults. T4519
`getContextState()`	function	Read the current context state from session-aware files. T4519
`sessionInit()`	function	Initialize orchestrator session state. Determines the recommended action base…
`shouldPause()`	function	Check if orchestrator should pause based on context usage. T4519
`analyzeDependencies()`	function	Analyze dependency graph and compute execution waves. T4519
`getNextTask()`	function	Get the next task ready to spawn for an epic. T4519
`getReadyTasks()`	function	Get all tasks ready to spawn in parallel (no inter-dependencies). T4519
`generateHitlSummary()`	function	Generate a Human-in-the-Loop summary for session handoff. T4519
`validateSubagentOutput()`	function	Validate a subagent’s manifest entry for protocol compliance. T4519
`validateManifestIntegrity()`	function	Validate the entire manifest file integrity. T4519
`verifyCompliance()`	function	Verify previous agent completed protocol compliance before spawning next. T4519
`validateOrchestratorCompliance()`	function	Validate orchestrator compliance (post-hoc behavioral checks). T4519
`getSkillSearchPaths()`	function	Get ordered skill search paths based on configuration. Priority: 1. CLEO_SKI…
`resolveSkillPath()`	function	Resolve a skill directory containing SKILL.md. Searches all paths from getSki…
`resolveProtocolPath()`	function	Resolve a protocol .md file. Search order: 1…
`resolveSharedPath()`	function	Resolve a shared resource .md file. Search order per base path:…
`getSkillSourceType()`	function	Classify the source of a skill directory. Determines where a skill directory…
`formatIsoDate()`	function	Format a date string in ISO 8601 format. Converts a YYYY-MM-DD date string to…
`getCurrentTimestamp()`	function	Get current timestamp in ISO 8601 format. Returns the current UTC time as an…
`isValidIsoDate()`	function	Validate that a string is a valid ISO 8601 date. T4552
`formatDateYMD()`	function	Format a Date object to a YYYY-MM-DD string. T4552
`validateSkill()`	function	Validate a skill directory structure and content. T4517
`validateSkills()`	function	Validate multiple skills at once. T4517
`validateReturnMessage()`	function	Validate a return message against protocol-compliant patterns. T4517
`getInstalledVersionAsync()`	function	Get the installed version of a skill from CAAMP lock state.
`checkSkillUpdateAsync()`	function	Check if a specific skill needs an update via CAAMP.
`checkAllSkillUpdatesAsync()`	function	Check all installed skills for available updates via CAAMP.
`exportSnapshot()`	function	Export current task state to a snapshot. T4882
`writeSnapshot()`	function	Write a snapshot to a file. T4882
`readSnapshot()`	function	Read a snapshot from a file. T4882
`getDefaultSnapshotPath()`	function	Generate a default snapshot file path. T4882
`importSnapshot()`	function	Import a snapshot into the local task database. Uses last-write-wins strategy…
`SpawnAdapterRegistry`	class	Registry to manage spawn adapters. Maintains mappings between adapter IDs, p…
`getProvidersWithSpawnCapability()`	function	Get providers by specific spawn capability Queries CAAMP for providers that…
`hasParallelSpawnProvider()`	function	Check if any provider supports parallel spawn
`initializeSpawnAdapters()`	function	Initialize spawn adapters dynamically from discovered adapter manifests. Sca…
`initializeDefaultAdapters()`	function	Initialize the registry with default adapters. Legacy entry point that disco…
`getWorkflowComplianceReport()`	function	Compute workflow compliance metrics from existing task, session, and audit da…
`getProjectStats()`	function	Get project statistics.
`rankBlockedTask()`	function	Compute a ranking score for a blocked task. Higher score = more urgent = sort…
`getDashboard()`	function	Get project dashboard data.
`getCompletionHistory()`	function	Get completion history data.
`filterByDate()`	function	Filter tasks by date range on archivedAt.
`summaryReport()`	function	Generate summary statistics.
`byPhaseReport()`	function	Group tasks by phase with cycle time averages.
`byLabelReport()`	function	Group tasks by label frequency.
`byPriorityReport()`	function	Group tasks by priority with cycle time averages.
`cycleTimesReport()`	function	Compute cycle time statistics with distribution buckets.
`trendsReport()`	function	Compute archive trends by day and month.
`analyzeArchive()`	function	Analyze archived tasks and produce a report. This is the primary entry point…
`getArchiveStats()`	function	Get archive statistics.
`auditData()`	function	Audit data integrity.
`createBackup()`	function	Create a backup of CLEO data files.
`listSystemBackups()`	function	List all available system backups (snapshot, safety, migration types). Reads…
`restoreBackup()`	function	Restore from a backup.
`cleanupSystem()`	function	Cleanup stale data (sessions, backups, logs).
`writeJsonFileAtomic()`	function	Write a JSON file atomically with backup rotation. Pattern: write temp - bac…
`readJsonFile()`	function	Read a JSON file, returning parsed content or null if not found.
`getDataPath()`	function	Get the path to a CLEO data file within a project root.
`resolveProjectRoot()`	function	Resolve the project root directory. Checks CLEO_ROOT env, then falls back to…
`withLock()`	function	Read and write a JSON file with exclusive locking. Acquires a cross-process…
`withFileLock()`	function	Acquire a file lock and execute an operation. Unlike withLock, this doesn’t r…
`withMultiLock()`	function	Acquire locks on multiple files in correct order. Used for operations that ne…
`isProjectInitialized()`	function	Check if a CLEO project directory exists at the given path
`listBackups()`	function	List backup files for a given data file
`detectPlatform()`	function	Detect the current platform.
`commandExists()`	function	Check if a command exists on PATH.
`requireTool()`	function	Require a tool to be available, returning an error message if missing.
`checkRequiredTools()`	function	Check all required tools.
`getIsoTimestamp()`	function	Get ISO 8601 UTC timestamp.
`isoToEpoch()`	function	Convert ISO timestamp to epoch seconds.
`dateDaysAgo()`	function	Get ISO date for N days ago.
`getFileSize()`	function	Get file size in bytes.
`getFileMtime()`	function	Get file modification time as ISO string.
`generateRandomHex()`	function	Generate N random hex characters.
`sha256()`	function	Compute SHA-256 checksum of a string.
`createTempFilePath()`	function	Create a temporary file path.
`getNodeVersionInfo()`	function	Get Node.js version info.
`getNodeUpgradeInstructions()`	function	Get platform-specific Node.js upgrade instructions. Returns actionable instal…
`getSystemInfo()`	function	Gather a snapshot of the host system. This is the SSoT for system informatio…
`checkCliInstallation()`	function	T4525
`checkCliVersion()`	function	T4525
`checkDocsAccessibility()`	function	T4525
`checkAtReferenceResolution()`	function	T4525
`checkAgentsMdHub()`	function	Check that AGENTS.md exists in project root and contains the CAAMP:START mark…
`checkRootGitignore()`	function	Check if project root .gitignore is blocking the entire .cleo/ directory. Thi…
`checkCleoGitignore()`	function	Check if .cleo/.gitignore exists and matches the template. T4700
`checkVitalFilesTracked()`	function	Check that vital CLEO configuration files are tracked by git. Only checks con…
`checkCoreFilesNotIgnored()`	function	Check that core CLEO files are not being ignored by .gitignore. Uses…
`checkSqliteNotTracked()`	function	Check that SQLite databases (.cleo/tasks.db) are NOT tracked by project git…
`checkLegacyAgentOutputs()`	function	Check if any legacy output directories still exist. Delegates detection to th…
`checkCaampMarkerIntegrity()`	function	Verify balanced CAAMP:START/END markers in CLAUDE.md and AGENTS.md. T5153
`checkAtReferenceTargetExists()`	function	Parse references from AGENTS.md CAAMP block and verify each target file exis…
`checkTemplateFreshness()`	function	Compare templates/CLEO-INJECTION.md vs ~/.cleo/templates/CLEO-INJECTION.md…
`checkTierMarkersPresent()`	function	Verify all 3 tier markers exist with matching close tags in deployed template…
`checkNodeVersion()`	function	Check that Node.js meets the minimum required version. Provides OS-specific u…
`checkGlobalSchemaHealth()`	function	Check that global schemas at ~/.cleo/schemas/ are installed and not stale. De…
`checkNoLocalSchemas()`	function	Warn if deprecated .cleo/schemas/ directory still exists in the project. Sche…
`checkJsonSchemaIntegrity()`	function	Check that active JSON files (config.json, project-info.json, etc.) are valid…
`runAllGlobalChecks()`	function	Run all global health checks and return results array. T4525
`calculateHealthStatus()`	function	Calculate overall status from check results. Returns: 0=passed, 50=warning, 5…
`getSystemHealth()`	function	Run system health checks (SQLite-first per ADR-006).
`getSystemDiagnostics()`	function	Run extended diagnostics with fix suggestions.
`coreDoctorReport()`	function	Run comprehensive doctor diagnostics combining dependency checks, directory c…
`runDoctorFixes()`	function	Run auto-fix for failed doctor checks by calling the corresponding ensure* fu…
`startupHealthCheck()`	function	Unified startup health check for CLI entry points. This is the single entry…
`generateInjection()`	function	Generate Minimum Viable Injection (MVI) markdown.
`getLabels()`	function	Get all labels with counts and task IDs per label.
`getSystemMetrics()`	function	Get system metrics: token usage, compliance summary, session counts.
`getMigrationStatus()`	function	Check/report schema migration status.
`getRuntimeDiagnostics()`	function
`safestop()`	function	Safe stop: signal clean shutdown for agents.
`uncancelTask()`	function	Uncancel a cancelled task (restore to pending).
`parseIssueTemplates()`	function	Parse all templates from the repo’s .github/ISSUE_TEMPLATE/ directory. Reads…
`getTemplateForSubcommand()`	function	Get template config for a specific subcommand (bug/feature/help). Performs a…
`generateTemplateConfig()`	function	Generate and cache the config as .cleo/issue-templates.json. Performs a live…
`validateLabels()`	function	Validate that labels exist on a GitHub repo. Compares the template labels ag…
`getCurrentShell()`	function	Detect the current shell.
`getRcFilePath()`	function	Get the RC file path for a shell.
`detectAvailableShells()`	function	Detect which shells are available on the system.
`generateBashAliases()`	function	Generate bash/zsh alias content.
`generatePowershellAliases()`	function	Generate PowerShell alias content.
`hasAliasBlock()`	function	Check if aliases are already injected in a file.
`getInstalledVersion()`	function	Get the installed alias version from an RC file.
`injectAliases()`	function	Inject aliases into a shell RC file.
`removeAliases()`	function	Remove aliases from a shell RC file.
`checkAliasesStatus()`	function	Get alias status for the current shell.
`discoverReleaseTasks()`	function	Discover task IDs for a release from completed tasks. Optionally filtered by…
`groupTasksIntoSections()`	function	Group tasks into changelog sections.
`generateChangelogMarkdown()`	function	Generate changelog markdown for a version.
`formatChangelogJson()`	function	Format changelog data as JSON.
`writeChangelogFile()`	function	Write changelog content to a file.
`appendToChangelog()`	function	Append a new release section to an existing CHANGELOG.md.
`generateChangelog()`	function	Full changelog generation: discover tasks, group, generate, write.
`parseCommandHeader()`	function	Parse a ###CLEO header block from a script file.
`scanAllCommands()`	function	Scan a scripts directory and build a command registry. Returns a map of comma…
`validateHeader()`	function	Validate a command header has required fields.
`getCommandScriptMap()`	function	Get command-to-script mapping.
`getCommandsByCategory()`	function	Group commands by category.
`getCommandsByRelevance()`	function	Filter commands by relevance level.
`defaultFlags()`	function	Default flag values.
`parseCommonFlags()`	function	Parse common CLI flags from an argument array. Returns flags and remaining po…
`resolveFormat()`	function	Resolve output format based on flags and TTY detection. Returns ‘json’ for no…
`isJsonOutput()`	function	Check if output should be JSON.
`checkManifestEntry()`	function	Verify a manifest entry for a task has valid required fields. T4524
`checkReturnFormat()`	function	Check if a response matches the expected return format. T4524
`scoreSubagentCompliance()`	function	Calculate comprehensive compliance score for a subagent. T4524
`calculateTokenEfficiency()`	function	Calculate token efficiency metrics. T4524
`calculateOrchestrationOverhead()`	function	Calculate orchestration overhead metrics. T4524
`getScriptCommands()`	function	Get command names from scripts directory. Returns sorted list of script basen…
`getIndexScripts()`	function	Get script names from COMMANDS-INDEX.json. T4527
`getIndexCommands()`	function	Get command names from COMMANDS-INDEX.json. T4527
`checkCommandsSync()`	function	Check commands index vs scripts directory for sync. T4527
`checkWrapperSync()`	function	Check wrapper template sync with COMMANDS-INDEX. T4527
`detectDrift()`	function	Run full drift detection across scripts, index, wrapper, and README. T4527
`shouldRunDriftDetection()`	function	Check if drift detection should run automatically based on config. T4527
`getCacheFilePath()`	function	Get cache file path. T4525
`initCacheFile()`	function	Initialize empty cache file. T4525
`loadCache()`	function	Load cache file or return null if missing/invalid. T4525
`getFileHash()`	function	Get file hash for cache invalidation. T4525
`getCachedValidation()`	function	Check if project validation is cached and valid. Returns the cache entry if v…
`cacheValidationResult()`	function	Cache project validation results. T4525
`clearProjectCache()`	function	Clear cache for a specific project. T4525
`clearEntireCache()`	function	Clear entire cache. T4525
`isTempProject()`	function	Check if a project path is a temporary/test directory. T4525
`categorizeProjects()`	function	Filter projects into categories: active, temp, orphaned. T4525
`getProjectCategoryName()`	function	Get human-readable project category name. T4525
`formatProjectHealthSummary()`	function	Format project health summary for display. T4525
`getProjectGuidance()`	function	Get actionable guidance for project issues. T4525
`getUserJourneyStage()`	function	Check user journey stage based on system state. T4525
`getJourneyGuidance()`	function	Get journey-specific guidance text. T4525
`sanitizeFilePath()`	function	Sanitize a file path for safe shell usage. Prevents command injection via mal…
`validateTitle()`	function	Validate a task title. Checks for emptiness, newlines, invisible characters,…
`validateDescription()`	function	T4523
`validateNote()`	function	T4523
`validateBlockedBy()`	function	T4523
`validateSessionNote()`	function	T4523
`validateCancelReason()`	function	Validate a cancellation reason. T4523
`validateStatusTransition()`	function	Validate that a status transition is allowed. T4523
`isValidStatus()`	function	Check if a status string is valid. T4523
`checkTimestampSanity()`	function	Check timestamp format and sanity. T4523
`isMetadataOnlyUpdate()`	function	Check if an update contains only metadata fields (safe for done tasks). T4523
`normalizeLabels()`	function	Deduplicate and normalize labels. T4523
`checkIdUniqueness()`	function	Check ID uniqueness within and across files. T4523
`validateTask()`	function	Validate a single task object. T4523
`validateNoCircularDeps()`	function	Check for circular dependencies using DFS. T4523
`validateSingleActivePhase()`	function	Validate only one phase is active. T4523
`validateCurrentPhaseConsistency()`	function	Validate currentPhase matches an active phase. T4523
`validatePhaseTimestamps()`	function	Validate phase timestamp ordering. T4523
`validatePhaseStatusRequirements()`	function	Validate phase status requirements (e.g., active phases must have startedAt)…
`validateAll()`	function	Run all validation checks on a TaskFile. T4523
`parseManifest()`	function	Parse a manifest JSONL content string into entries. Skips invalid JSON lines gracefully…
`findReviewDocs()`	function	Find documents in review status. T4524
`extractTopics()`	function	Extract markdown headings from file content. T4524
`searchCanonicalCoverage()`	function	Search for topic coverage in a docs directory. Returns count of matching file…
`analyzeCoverage()`	function	Analyze documentation coverage for review documents. T4524
`formatGapReport()`	function	Format a gap report for human-readable display. T4524
`findManifestEntry()`	function	Find a manifest entry for a task ID in a JSONL file. T4526
`validateManifestEntry()`	function	Run validation on a manifest entry for a specific task. T4526
`logRealCompliance()`	function	Log validation results to the compliance JSONL file. T4526
`validateAndLog()`	function	Find, validate, and log compliance for a task in one call. T4526
`checkOutputFileExists()`	function	Check if expected output file exists. T4527
`checkDocumentationSections()`	function	Check if file contains required documentation sections. T4527
`checkReturnMessageFormat()`	function	Check if return message follows protocol format. Expected: ” . See MANIFEST.j…
`checkManifestFieldPresent()`	function	Check if manifest entry has a required field (non-null, non-empty). T4527
`checkManifestFieldType()`	function	Check if manifest field has expected type. T4527
`checkKeyFindingsCount()`	function	Check if key_findings array has valid count (3-7). T4527
`checkStatusValid()`	function	Check if status is valid enum value. T4527
`checkAgentType()`	function	Check if agent_type matches expected value. T4527
`checkLinkedTasksPresent()`	function	Check if linked_tasks array contains required task IDs. T4527
`checkProvenanceTags()`	function	Check if file contains provenance tag. T4527
`validateCommonManifestRequirements()`	function	Validate common manifest requirements across all protocols. When protocolTyp…
`isValidGateName()`	function	T4526
`isValidAgentName()`	function	T4526
`getGateOrder()`	function	T4526
`getGateIndex()`	function	T4526
`getDownstreamGates()`	function	T4526
`initVerification()`	function	Initialize a new verification object with default values. T4526
`computePassed()`	function	Compute whether verification has passed based on required gates. T4526
`setVerificationPassed()`	function	Update the passed field on a verification object. T4526
`updateGate()`	function	Update a single gate value. T4526
`resetDownstreamGates()`	function	Reset all downstream gates to null after a gate failure. T4526
`incrementRound()`	function	Increment the round counter. Returns null if max rounds exceeded. T4526
`logFailure()`	function	Log a failure to the failureLog array. T4526
`checkAllGatesPassed()`	function	Check if all required gates have passed. T4526
`isVerificationComplete()`	function	Check if verification is complete (passed = true). T4526
`getVerificationStatus()`	function	Get verification status for display. T4526
`shouldRequireVerification()`	function	Check if a task type should require verification. T4526
`getMissingGates()`	function	Get gate names that are not yet true. T4526
`getGateSummary()`	function	Get gate summary for display. T4526
`checkCircularValidation()`	function	Check for circular validation (self-approval prevention). Prevents: creator v…
`allEpicChildrenVerified()`	function	Check if all children of an epic have verification.passed = true. T4526
`allSiblingsVerified()`	function	Check if all siblings of a task are verified. T4526
`getProjectInfo()`	function	Read project-info.json and return a typed ProjectInfo. Falls back gracefully…
`getProjectInfoSync()`	function	Synchronous variant for use in hot paths where async is not feasible. Returns…
`updateProjectName()`	function	Update the project name in project-info.json. Used by `cleo upgrade --name` a…
`generateAcFromDescription()`	function	Generate 3 baseline acceptance criteria from a task description. Uses simple…
`backfillTasks()`	function	Retroactively populate AC and verification metadata for tasks that lack them.
`ProtocolEnforcer`	class	Main protocol enforcement class
`getHookCapableProviders()`	function	Get all providers that support a specific hook event
`getSharedHookEvents()`	function	Get hook events supported by all specified providers
`toNativeHookEvent()`	function	Translate a canonical hook event to a provider-native event name.
`toCanonicalHookEvent()`	function	Translate a provider-native event name back to its canonical equivalent.
`providerSupportsHookEvent()`	function	Check if a provider supports a specific canonical hook event.
`validateChainShape()`	function	Validate the topology/DAG of a chain shape. Checks: - All link source/target…
`validateGateSatisfiability()`	function	Validate that all gates in a chain reference valid stages and gate names. Ch…
`validateChain()`	function	Validate a complete WarpChain definition. Orchestrates shape validation and…
`addChain()`	function	Store a validated WarpChain definition. Validates the chain before storing…
`showChain()`	function	Retrieve a WarpChain definition by ID. T5403
`listChains()`	function	List all stored WarpChain definitions. T5403
`findChains()`	function	Find WarpChain definitions by criteria. T5403
`createInstance()`	function	Create a chain instance binding a chain to an epic. T5403
`showInstance()`	function	Retrieve a chain instance by ID. T5403
`listInstanceGateResults()`	function	Read persisted gate results for a chain instance.
`advanceInstance()`	function	Advance a chain instance to the next stage, recording gate results. T5403
`validateResearchProtocol()`	function	T4499
`validateConsensusProtocol()`	function	T4499
`validateSpecificationProtocol()`	function	T4499
`validateDecompositionProtocol()`	function	T4499
`validateImplementationProtocol()`	function	T4499
`validateContributionProtocol()`	function	T4499
`validateReleaseProtocol()`	function	T4499
`validateArtifactPublishProtocol()`	function	T4499
`validateProvenanceProtocol()`	function	T4499
`validateArchitectureDecisionProtocol()`	function	Validate an Architecture Decision Record manifest entry. Enforces the 8 MUST…
`validateValidationProtocol()`	function	Validate a manifest entry against the validation stage protocol. Enforces VA…
`validateTestingProtocol()`	function	Validate a manifest entry against the testing protocol. This validator is **…
`validateProtocol()`	function	Validate a manifest entry against a specific protocol. Throws CleoError with…
`buildDefaultChain()`	function	Build the canonical 9-stage RCASD-IVTR+C WarpChain. - Each PIPELINE_STAGE be…
`buildDefaultTessera()`	function	Build the default RCASD Tessera template. Wraps buildDefaultChain() with tem…
`instantiateTessera()`	function	Instantiate a Tessera template into a concrete WarpChainInstance. Steps: 1…
`listTesseraTemplates()`	function	List all registered Tessera templates. T5409
`showTessera()`	function	Find a Tessera template by ID. T5409
`runBrainMaintenance()`	function	Run a combined brain maintenance pass: decay, consolidation, and embeddings…
`migrateClaudeMem()`	function	Migrate observations from claude-mem’s SQLite database into CLEO brain.db. R…
`reasonWhy()`	function	Build a causal trace for why a task is blocked. Walks upstream through…
`reasonSimilar()`	function	Find entries similar to a given brain.db entry. 1. Loads the source entry’s…
`memoryShow()`	function	Look up a brain.db entry by ID.
`memoryBrainStats()`	function	Aggregate stats from brain.db across all tables.
`memoryDecisionFind()`	function	Search decisions in brain.db.
`memoryDecisionStore()`	function	Store a decision to brain.db.
`memoryFind()`	function	Token-efficient brain search returning compact results.
`memoryTimeline()`	function	Chronological context around a brain entry anchor.
`memoryFetch()`	function	Batch fetch brain entries by IDs.
`memoryObserve()`	function	Save an observation to brain.db.
`memoryPatternStore()`	function	Store a pattern to BRAIN memory.
`memoryPatternFind()`	function	Search patterns in BRAIN memory.
`memoryPatternStats()`	function	Get pattern memory statistics.
`memoryLearningStore()`	function	Store a learning to BRAIN memory.
`memoryLearningFind()`	function	Search learnings in BRAIN memory.
`memoryLearningStats()`	function	Get learning memory statistics.
`memoryContradictions()`	function	Find contradictory entries in brain.db.
`memorySuperseded()`	function	Find superseded entries in brain.db. Identifies entries that have been super…
`memoryLink()`	function	Link a brain entry to a task.
`memoryUnlink()`	function	Remove a link between a brain entry and a task.
`memoryGraphAdd()`	function	Add a node or edge to the PageIndex graph.
`memoryGraphShow()`	function	Get a node and its edges from the PageIndex graph.
`memoryGraphNeighbors()`	function	Get neighbor nodes from the PageIndex graph.
`memoryReasonWhy()`	function	Causal trace through task dependency chains.
`memoryReasonSimilar()`	function	Find semantically similar entries.
`memorySearchHybrid()`	function	Hybrid search across FTS5, vector, and graph.
`memoryGraphRemove()`	function	Remove a node or edge from the PageIndex graph.
`pipelineManifestShow()`	function	pipeline.manifest.show - Get manifest entry details by ID
`pipelineManifestList()`	function	pipeline.manifest.list - List manifest entries with filters
`pipelineManifestFind()`	function	pipeline.manifest.find - Find manifest entries by text (LIKE search on conten…
`pipelineManifestPending()`	function	pipeline.manifest.pending - Get pending manifest items
`pipelineManifestStats()`	function	pipeline.manifest.stats - Manifest statistics
`pipelineManifestRead()`	function	pipeline.manifest.read - Read manifest entries with optional filter
`pipelineManifestAppend()`	function	pipeline.manifest.append - Append entry to pipeline_manifest table
`pipelineManifestArchive()`	function	pipeline.manifest.archive - Archive old manifest entries by date
`pipelineManifestCompact()`	function	pipeline.manifest.compact - Dedup by contentHash (keep newest by createdAt)
`pipelineManifestValidate()`	function	pipeline.manifest.validate - Validate manifest entries for a task
`pipelineManifestContradictions()`	function	pipeline.manifest.contradictions - Find entries with overlapping topics but c…
`pipelineManifestSuperseded()`	function	pipeline.manifest.superseded - Identify entries replaced by newer work on sam…
`pipelineManifestLink()`	function	pipeline.manifest.link - Link manifest entry to a task
`readManifestEntries()`	function	Read all manifest entries from the pipeline_manifest table. Replaces readMani…
`filterEntries()`	function	Filter manifest entries by criteria (alias for backward compatibility).
`distillManifestEntry()`	function	Distill a manifest entry to brain.db observation (Phase 3, pending).
`migrateManifestJsonlToSqlite()`	function	Migrate existing legacy flat-file entries into the pipeline_manifest table…
`resolveProviderFromModelIndex()`	function
`resolveProviderFromModelRegistry()`	function
`resetModelsDevCache()`	function
`measureTokenExchange()`	function
`recordTokenExchange()`	function
`showTokenUsage()`	function
`listTokenUsage()`	function
`summarizeTokenUsage()`	function
`deleteTokenUsage()`	function
`clearTokenUsage()`	function
`autoRecordDispatchTokenUsage()`	function
`getLatestTokenRecord()`	function
`getTokenUsageAggregateSql()`	function
`startParallelExecution()`	function	Start parallel execution for a wave.
`endParallelExecution()`	function	End parallel execution for a wave.
`getParallelStatus()`	function	Get current parallel execution state.
`listSkills()`	function	List available skills from canonical and project-local directories.
`getSkillContent()`	function	Read skill content for injection into agent context. Checks project-local ski…
`getUnblockOpportunities()`	function	Analyze dependency graph for unblocking opportunities.
`validateSpawnReadiness()`	function	Validate spawn readiness for a task.
`injectContext()`	function	Read protocol injection content for a given protocol type. Core logic for ses…
`generateSessionId()`	function	Generate a canonical session ID. Format: ses_YYYYMMDDHHmmss_6hex Example: se…
`isValidSessionId()`	function	Check if a string is a valid session ID (any format).
`isCanonicalSessionId()`	function	Check if a session ID uses the canonical format.
`extractSessionTimestamp()`	function	Extract an approximate timestamp from any valid session ID format. Returns nu…
`createSession()`	function	Create a new session.
`getSession()`	function	Get a session by ID.
`updateSession()`	function	Update a session.
`listSessions()`	function	List sessions with optional filters.
`endSession()`	function	End a session.
`startTask()`	function	Start working on a task within a session.
`getCurrentTask()`	function	Get current task for a session.
`stopTask()`	function	Stop working on the current task for a session.
`workHistory()`	function	Get work history for a session.
`gcSessions()`	function	Garbage collect old sessions (mark ended sessions as orphaned after threshold).
`getActiveSession()`	function	Get the currently active session (if any).
`suggestRelated()`	function	Suggest related tasks based on shared attributes.
`addRelation()`	function	Add a relation between tasks.
`discoverRelated()`	function	Discover related tasks using various methods.
`listRelations()`	function	List existing relations for a task.
`canCancel()`	function	Check if a task can be cancelled.
`cancelTask()`	function	Cancel a task in the tasks array (returns updated array). Does NOT handle chi…
`cancelMultiple()`	function	Batch cancel multiple tasks.
`coreTaskNext()`	function	Suggest next task to work on based on priority, phase, age, and deps.
`coreTaskBlockers()`	function	Show blocked tasks and analyze blocking chains.
`coreTaskTree()`	function	Build hierarchy tree for tasks.
`coreTaskDeps()`	function	Show dependencies for a task.
`coreTaskRelates()`	function	Show task relations.
`coreTaskRelatesAdd()`	function	Add a relation between two tasks.
`coreTaskAnalyze()`	function	Analyze tasks for priority and leverage.
`coreTaskRestore()`	function	Restore a cancelled task back to pending.
`coreTaskCancel()`	function	Cancel a task (sets status to ‘cancelled’, a soft terminal state). Use restor…
`coreTaskUnarchive()`	function	Move an archived task back to active tasks.
`coreTaskReorder()`	function	Change task position within its sibling group.
`coreTaskReparent()`	function	Move task under a different parent.
`coreTaskPromote()`	function	Promote a subtask to task or task to root.
`coreTaskReopen()`	function	Reopen a completed task.
`coreTaskComplexityEstimate()`	function	Deterministic complexity scoring from task metadata.
`coreTaskDepsOverview()`	function	Overview of all dependencies across the project.
`coreTaskDepsCycles()`	function	Detect circular dependencies across the project.
`coreTaskDepends()`	function	List dependencies for a task in a given direction.
`coreTaskStats()`	function	Compute task statistics.
`coreTaskExport()`	function	Export tasks as JSON or CSV.
`coreTaskHistory()`	function	Get task history from the audit log.
`coreTaskLint()`	function	Lint tasks for common issues.
`coreTaskBatchValidate()`	function	Validate multiple tasks at once.
`coreTaskImport()`	function	Import tasks from a JSON source string.
`analyzeTaskPriority()`	function	Analyze task priority with leverage scoring.
`listLabels()`	function	List all labels with task counts.
`showLabelTasks()`	function	Show tasks with a specific label.
`getLabelStats()`	function	Get detailed label statistics.
`createStoreProvider()`	function	Create a store provider. Always creates SQLite provider (ADR-006). T4647
`getStore()`	function	Get a StoreProvider instance for the given working directory. Convenience wra…
`countJsonRecords()`	function	Count records in JSON source files.
`migrateJsonToSqliteAtomic()`	function	Migrate JSON data to SQLite with atomic rename pattern. Writes to a temporary…
`migrateJsonToSqlite()`	function
`exportToJson()`	function	Export SQLite data back to JSON format (for inspection or emergency recovery).
`repairMissingSizes()`	function	Set size=‘medium’ on tasks that have no size value. Operates directly on the…
`repairMissingCompletedAt()`	function	Set completedAt=now() on done/cancelled tasks that are missing a completedAt…
`repairMissingColumns()`	function	Detect and add missing required columns on the tasks table. Uses PRAGMA table…
`runAllRepairs()`	function	Run all repair functions. Returns all actions taken (or previewed in dry-run…
`runUpgrade()`	function	Run a full upgrade pass on the project .cleo/ directory. Steps: 1. Pre-fli…
`diagnoseUpgrade()`	function	Deep diagnostic inspection of schema and migration state. Unlike bare…
`VerificationGate`	class	Main Verification Gate class Orchestrates 4-layer validation and determines…
`createVerificationGate()`	function	Factory function for creating verification gates
`WorkflowGateTracker`	class	WorkflowGateTracker Tracks the status of all 6 workflow verification gates f…
`isValidWorkflowGateName()`	function	Validate a workflow gate name string
`getWorkflowGateDefinition()`	function	Get the definition for a workflow gate
`validateLayer1Schema()`	function	Layer 1: Schema Validation Validates operation parameters against JSON Schem…
`validateLayer2Semantic()`	function	Layer 2: Semantic Validation Validates business rules and logical constraints.
`validateLayer3Referential()`	function	Layer 3: Referential Validation Validates cross-entity references and relati…
`validateLayer4Protocol()`	function	Layer 4: Protocol Validation Validates RCASD-IVTR+C lifecycle compliance and…
`isFieldRequired()`	function	Helper to check if a field is required for an operation
`validateWorkflowGateName()`	function	Validate a workflow gate name T3141
`validateWorkflowGateStatus()`	function	Validate a workflow gate status value per Section 7.3 T3141
`validateWorkflowGateUpdate()`	function	Validate a gate update operation. T3141
`buildMcpInputSchema()`	function	Build a JSON Schema `input_schema` object from an `OperationDef`. Algorithm:…
`buildCommanderArgs()`	function	Split `OperationDef.params` into positional arguments and option flags, suita…
`buildCommanderOptionString()`	function	Build the Commander option string for a single non-positional ParamDef. Exam…
`camelToKebab()`	function	Convert a camelCase string to kebab-case. e.g. ‘includeArchive’ → ‘include-ar…
`validateRequiredParamsDef()`	function	Validates that all required parameters are present in the request. Returns an…
`findManifestEntry()`	function	Locate the manifest line for a given task ID, reading from the end of the fil…
`loadManifestEntryByTaskId()`	function	Load a manifest entry by task ID from the canonical manifest file. T260
`loadManifestEntryFromFile()`	function	Load a manifest entry from an arbitrary JSON file (used by the `manifest` dis…
`throwIfStrictFailed()`	function	Throw a CleoError with the protocol’s canonical exit code when strict validat…
`validateArchitectureDecisionTask()`	function	Validate architecture-decision protocol for a task.
`checkArchitectureDecisionManifest()`	function	Validate architecture-decision protocol from a manifest file.
`validateArtifactPublishTask()`	function	Validate artifact-publish protocol for a task.
`checkArtifactPublishManifest()`	function	Validate artifact-publish protocol from a manifest file.
`validateConsensusTask()`	function	Validate consensus protocol for a task.
`checkConsensusManifest()`	function	Validate consensus protocol from a manifest file.
`validateContributionTask()`	function	Validate contribution protocol for a task.
`checkContributionManifest()`	function	Validate contribution protocol from a manifest file.
`validateDecompositionTask()`	function	Validate decomposition protocol for a task.
`checkDecompositionManifest()`	function	Validate decomposition protocol from a manifest file.
`validateImplementationTask()`	function	Validate implementation protocol for a task.
`checkImplementationManifest()`	function	Validate implementation protocol from a manifest file.
`validateProvenanceTask()`	function	Validate provenance protocol for a task.
`checkProvenanceManifest()`	function	Validate provenance protocol from a manifest file.
`validateReleaseTask()`	function	Validate release protocol for a task.
`checkReleaseManifest()`	function	Validate release protocol from a manifest file.
`validateResearchTask()`	function	Validate research protocol for a task.
`checkResearchManifest()`	function	Validate research protocol from a manifest file.
`validateSpecificationTask()`	function	Validate specification protocol for a task.
`checkSpecificationManifest()`	function	Validate specification protocol from a manifest file.
`validateTestingTask()`	function	Validate testing protocol for a task.
`checkTestingManifest()`	function	Validate testing protocol from a manifest file.
`validateValidationTask()`	function	Validate validation-stage protocol for a task.
`checkValidationManifest()`	function	Validate validation-stage protocol from a manifest file.
`validateSchema()`	function	Validate data against a CLEO schema
`validateTask()`	function	Validate a single task object against the drizzle-zod insert schema. Uses dri…
`clearSchemaCache()`	function	Clear the schema cache (useful for testing)
`coreValidateReport()`	function	Run comprehensive validation report on tasks database — checks business rules…
`coreValidateAndFix()`	function	Run validation report, then apply data repairs for fixable issues. Calls runA…
`coreValidateSchema()`	function	Validate data against a schema type. For SQLite-backed types (todo, archive,…
`coreValidateTask()`	function	Validate a single task against anti-hallucination rules. T4786
`coreValidateProtocol()`	function	Check basic protocol compliance for a task. T4786
`coreValidateManifest()`	function	Validate manifest JSONL entries for required fields. T4786
`coreValidateOutput()`	function	Validate an output file for required sections. T4786
`coreComplianceSummary()`	function	Get aggregated compliance metrics. T4786
`coreComplianceViolations()`	function	List compliance violations. T4786
`coreComplianceRecord()`	function	Record a compliance check result to COMPLIANCE.jsonl. T4786
`coreTestStatus()`	function	Check test suite availability. T4786
`coreCoherenceCheck()`	function	Cross-validate task graph for consistency. T4786
`coreTestRun()`	function	Execute test suite via subprocess. T4786
`coreBatchValidate()`	function	Batch validate all tasks against schema and rules. T4786
`coreTestCoverage()`	function	Get test coverage metrics. T4786
`buildBrainState()`	function	Build brain state for agent bootstrapping.
`getCriticalPath()`	function	Find the critical path (longest dependency chain) in the task graph.
`resolveSkillPathsForProvider()`	function	Get effective skill paths for a provider considering precedence
`getProvidersWithPrecedence()`	function	Get all providers that use a specific precedence mode
`getSkillsMapWithPrecedence()`	function	Build complete skills map with precedence information
`determineInstallationTargets()`	function	Determine target installation paths for a skill
`supportsAgentsPath()`	function	Check if provider supports agents path
`coreTaskPlan()`	function	Build composite planning view. T4914
`encrypt()`	function	Encrypt a plaintext string using AES-256-GCM with a per-project key. Output…
`decrypt()`	function	Decrypt a base64-encoded ciphertext using AES-256-GCM with a per-project key.
`AgentRegistryAccessor`	class	signaldock.db implementation of the AgentRegistryAPI.
`buildIndex()`	function	Scan .cleo/rcasd/ and legacy .cleo/rcsd/ directories and build the RCASD inde…
`writeIndex()`	function	Write RCASD-INDEX.json to disk.
`readIndex()`	function	Read RCASD-INDEX.json from disk.
`rebuildIndex()`	function	Rebuild and write the index from current disk state.
`getTaskAnchor()`	function	Get task anchor by task ID.
`findByStage()`	function	Find tasks by pipeline stage.
`findByStatus()`	function	Find tasks by status.
`getIndexTotals()`	function	Get index summary statistics.
`ApprovalManager`	class	Manages approval tokens for CANT workflow gates. Tokens are stored in-memory…
`createScope()`	function	Creates a new root execution scope with initial variable bindings.
`createChildScope()`	function	Creates a child scope that inherits from a parent. Lookups in the child scop…
`resolveVariable()`	function	Resolves a variable name in the scope chain. Searches the current scope firs…
`setVariable()`	function	Sets a variable in the current scope (does not affect parent scopes).
`resolveTemplate()`	function	Resolves `{variable}` placeholders in a template string against the scope. P…
`mergeStepOutput()`	function	Merges step output into the current scope. Binds `<stepName>.stdout`,…
`flattenScope()`	function	Collects all variable bindings visible from the given scope (including parent…
`DefaultDiscretionEvaluator`	class	Default discretion evaluator that always returns `true`. This is a stub impl…
`MockDiscretionEvaluator`	class	Mock discretion evaluator with configurable responses for testing. Responses…
`RateLimitedDiscretionEvaluator`	class	Wraps a discretion evaluator with rate limiting. Enforces a configurable max…
`executeParallel()`	function	Executes parallel arms according to the specified join strategy.
`WorkflowExecutor`	class	Executes CANT workflow definitions. The executor processes each statement in…
`generateCodebaseMapSummary()`	function
`sequenceChains()`	function	Sequence two chains: connect A’s exit points to B’s entry point. B’s stage I…
`parallelChains()`	function	Compose chains in parallel with a common fork entry and join stage. Creates…
`resolveEpicFromContent()`	function	Extract an epic/task ID from file content by searching for: 1…
`resolveEpicFromFilename()`	function	Extract an epic ID from a filename pattern like `T####-` or `T####_`.
`normalizeDirectoryNames()`	function	Rename suffixed epic directories (e.g. `T4881_install-channels` → `T4881`).
`migrateConsensusFiles()`	function	Migrate `.cleo/consensus/` files to appropriate epic’s consensus/ subdirector…
`migrateContributionFiles()`	function	Migrate `.cleo/contributions/` files to appropriate epic’s contributions/ sub…
`migrateLooseFiles()`	function	Migrate loose `T####_*.md` files from `.cleo/rcasd/` root into…
`consolidateRcasd()`	function	Consolidate all provenance files into the unified `.cleo/rcasd/{epicId}/` str…
`findResumablePipelines()`	function	Query active pipelines that can be resumed. Searches the lifecycle_pipelines…
`loadPipelineContext()`	function	Load complete pipeline context for session resume. Uses SQL JOINs to efficie…
`resumeStage()`	function	Resume a specific stage in a pipeline. Updates the stage status from ‘blocke…
`autoResume()`	function	Auto-detect where to resume across all active pipelines. Finds the best cand…
`checkSessionResume()`	function	Check for resumable work on session start. Integrates with session initializ…
`formatResumeSummary()`	function	Get resume summary for display to user. Formats resumable pipelines into a h…
`handleCompletedStage()`	function	Handle completed stage edge case. If the current stage is completed, suggest…
`handleBlockedStage()`	function	Handle blocked stage edge case. Provides information about why a stage is bl…
`checkBlockedStageDetails()`	function	Handle blocked stage edge case - async version with database lookup.
`checkPrerequisites()`	function	Check if prerequisites are met for a stage. Validates that all prerequisite…
`validateTransition()`	function	Validate a stage transition. Comprehensive validation that checks both trans…
`executeTransition()`	function	Execute a state transition. Applies the transition to the state machine cont…
`setStageStatus()`	function	Set the status of a stage. Updates stage status with validation of allowed s…
`getStageStatus()`	function	Get the status of a stage.
`isValidStatusTransition()`	function	Check if a status transition is valid. State transitions: not_started → in…
`createInitialContext()`	function	Create initial state machine context for a pipeline.
`getValidNextStages()`	function	Get stages that can be transitioned to from the current stage.
`getCurrentStageState()`	function	Get the current stage state.
`isTerminalState()`	function	Check if the pipeline is in a terminal state.
`isBlocked()`	function	Check if the pipeline is blocked.
`validateTransitions()`	function	Validate multiple transitions.
`canSkipStage()`	function	Check if a stage can be skipped.
`skipStage()`	function	Skip a stage with validation.
`EmbeddingQueue`	class	Singleton embedding queue. Batches embedding requests and processes them via…
`getEmbeddingQueue()`	function	Get or create the shared EmbeddingQueue singleton. Registers a process…
`resetEmbeddingQueue()`	function	Reset the singleton (for testing only). Shuts down the existing queue before…
`getContextStatusFromPercentage()`	function	Determine status from percentage.
`processContextInput()`	function	Process context window input and write state file. Returns the status line st…
`isHITLEnabled()`	function	Check if HITL warnings are enabled.
`generateHITLWarnings()`	function	Generate HITL warnings based on lock state.
`getHighestLevel()`	function	Get highest warning level from warnings.
`getConcurrencyJson()`	function	Get concurrency data for analyze JSON output.
`checkStatuslineIntegration()`	function	Check if statusline integration is configured. Returns the current integratio…
`getStatuslineConfig()`	function	Get the statusline setup command for Claude Code settings.
`getSetupInstructions()`	function	Get human-readable setup instructions.
`getPreferredChannel()`	function	Look up the preferred channel for a given domain + operation. Reads from the…
`getRoutingForDomain()`	function	Get routing entries for a specific domain. Derives entries from the capabili…
`getOperationsByChannel()`	function	Get all operations that prefer a specific channel. Derives entries from the…
`generateMemoryProtocol()`	function	Generate dynamic memory protocol instructions based on provider capabilities.
`generateRoutingGuide()`	function	Generate a dynamic routing guide based on operation preferences.
`generateDynamicSkillContent()`	function	Generate complete dynamic skill content for the current provider.
`TaskCache`	class	In-memory cache for task indices with checksum-based staleness detection.
`extractPackageMeta()`	function	Extract package metadata from an export file. T4552
`logImportStart()`	function	Log import operation start with package metadata. T4552
`logImportSuccess()`	function	Log import operation completion with full metadata. T4552
`logImportError()`	function	Log import operation error with diagnostic details. T4552
`logImportConflict()`	function	Log import conflict detection and resolution. T4552
`topologicalSortTasks()`	function	Topological sort for task import order using Kahn’s algorithm. Ensures tasks…
`detectCycles()`	function	Detect cycles in task dependency graph. Returns true if no cycles, false if c…
`findActivePipelinesWithStagesAndTasks()`	function	Find active pipelines joined with their stages and tasks. Optionally filters…
`findPipelineWithCurrentStageAndTask()`	function	Find a pipeline with its current stage and task by taskId. Matches stages whe…
`findPipelineWithStage()`	function	Find a pipeline and a specific stage by taskId and stageName.
`updatePipelineCurrentStage()`	function	Update pipeline’s currentStageId.
`getStagesByPipelineId()`	function	Get all stages for a pipeline, ordered by sequence.
`activateStage()`	function	Update a stage’s status to ‘in_progress’ and clear block fields.
`findPipelineWithCurrentStage()`	function	Find pipeline with current stage (no task join) by taskId. Used by checkBlock…
`getGateResultsByStageId()`	function	Get gate results for a stage, ordered by checkedAt descending.
`getGateResultsByStageIdUnordered()`	function	Get gate results for a stage without ordering (for simple checks).
`getEvidenceByStageId()`	function	Get evidence for a stage, ordered by recordedAt descending.
`getRecentTransitions()`	function	Get recent transitions for a pipeline, ordered by createdAt descending.
`insertTransition()`	function	Insert a new transition record.
`checkAtomicity()`	function	Check task atomicity using 6-point heuristic test. Default threshold: 4 (pass…
`extractTaskRefs()`	function	Extract task IDs from text content. Scans for patterns like T1234, T001, T42…
`createRelatesEntries()`	function	Create relates entries from extracted task IDs.
`mergeRelatesArrays()`	function	Merge new relates entries with existing ones. Existing entries take precedenc…
`validateRelatesRefs()`	function	Validate that referenced task IDs exist. Returns array of invalid (non-existe…
`extractAndCreateRelates()`	function	Convenience: extract task refs from text and create relates entries.
`calculateAffectedTasks()`	function	Calculate which tasks would be affected by a delete operation.
`calculateImpact()`	function	Calculate impact of deletion.
`generateWarnings()`	function	Generate warnings based on impact analysis.
`previewDelete()`	function	Main preview function - coordinates all preview calculations.
`isValidStrategy()`	function	Validate a strategy name.
`handleChildren()`	function	Handle children using the specified strategy. Returns the modified tasks arra…
`GraphCache`	class	Graph cache for expensive dependency calculations. Automatically invalidates…
`discoverByLabels()`	function	Discover related tasks by shared labels.
`discoverByDescription()`	function	Discover related tasks by description similarity (keyword-based Jaccard).
`discoverByFiles()`	function	Discover related tasks by shared files.
`discoverByHierarchy()`	function	Discover related tasks by hierarchical proximity (siblings and cousins).
`discoverRelatedTasks()`	function	Discover related tasks using all methods combined.
`suggestRelates()`	function	Suggest relates entries filtered by threshold.
`getCurrentPhase()`	function	Get the current active phase from project metadata.
`getTasksByPhase()`	function	Get tasks belonging to a specific phase.
`calculatePhaseProgress()`	function	Calculate progress for a phase.
`getAllPhaseProgress()`	function	Get progress for all phases.
`validatePhaseTransition()`	function
`createPhaseTransition()`	function	Create a phase transition record.
`applyPhaseTransition()`	function	Apply a phase transition to project metadata. Returns updated project data.
`getNextPhase()`	function	Get the next phase in order.
`allPhasesComplete()`	function	Check if all phases are complete.
`getSizeWeight()`	function	Get weight for a task size.
`getPriorityWeight()`	function	Get weight for a task priority.
`calculateTaskScore()`	function	Calculate a composite score for task ordering. Higher score = should be worke…
`sortByWeight()`	function	Sort tasks by weighted score (highest first).
`calculateTotalEffort()`	function	Calculate total weighted effort for a set of tasks.
`calculateWeightedProgress()`	function	Calculate completion percentage by weight.
`calculateRemainingEffort()`	function	Estimate remaining effort (weighted sum of non-complete tasks).
`getLastActivity()`	function	Get the most recent activity timestamp for a task.
`classifyStaleness()`	function	Classify staleness level for a task.
`getStalenessInfo()`	function	Get staleness info for a single task.
`findStaleTasks()`	function	Find all stale tasks (stale, critical, or abandoned).
`getStalenessSummary()`	function

Types & Interfaces

Symbol	Kind	Description
`LoggerConfig`	interface
`PlatformPaths`	interface	OS-appropriate paths for CLEO’s global directories.
`SystemInfo`	interface	Immutable system information snapshot, captured once per process.
`RequiredColumn`	interface	Required column definition for ensureColumns().
`VacuumOptions`	interface
`AgentInstanceRow`	type
`NewAgentInstanceRow`	type
`AgentErrorLogRow`	type
`NewAgentErrorLogRow`	type
`AgentInstanceStatus`	type
`AgentType`	type
`AgentErrorType`	type
`WarpChainRow`	type
`NewWarpChainRow`	type
`WarpChainInstanceRow`	type
`NewWarpChainInstanceRow`	type
`StatusRegistryRow`	type
`TaskRow`	type
`NewTaskRow`	type
`SessionRow`	type
`NewSessionRow`	type
`TaskDependencyRow`	type
`TaskRelationRow`	type
`WorkHistoryRow`	type
`LifecyclePipelineRow`	type
`NewLifecyclePipelineRow`	type
`LifecycleStageRow`	type
`NewLifecycleStageRow`	type
`LifecycleGateResultRow`	type
`NewLifecycleGateResultRow`	type
`LifecycleEvidenceRow`	type
`NewLifecycleEvidenceRow`	type
`LifecycleTransitionRow`	type
`NewLifecycleTransitionRow`	type
`AuditLogRow`	type
`NewAuditLogRow`	type
`TokenUsageRow`	type
`NewTokenUsageRow`	type
`ArchitectureDecisionRow`	type
`NewArchitectureDecisionRow`	type
`AdrTaskLinkRow`	type
`NewAdrTaskLinkRow`	type
`AdrRelationRow`	type
`NewAdrRelationRow`	type
`ManifestEntryRow`	type
`NewManifestEntryRow`	type
`PipelineManifestRow`	type
`NewPipelineManifestRow`	type
`ReleaseManifestRow`	type
`NewReleaseManifestRow`	type
`ExternalTaskLinkRow`	type
`NewExternalTaskLinkRow`	type
`BrainDecisionRow`	type
`NewBrainDecisionRow`	type
`BrainPatternRow`	type
`NewBrainPatternRow`	type
`BrainLearningRow`	type
`NewBrainLearningRow`	type
`BrainObservationRow`	type
`NewBrainObservationRow`	type
`BrainMemoryLinkRow`	type
`NewBrainMemoryLinkRow`	type
`BrainPageNodeRow`	type
`NewBrainPageNodeRow`	type
`BrainPageEdgeRow`	type
`NewBrainPageEdgeRow`	type
`BrainStickyNoteRow`	type
`NewBrainStickyNoteRow`	type
`ProjectRegistryRow`	type
`NewProjectRegistryRow`	type
`NexusAuditLogRow`	type
`NewNexusAuditLogRow`	type
`NexusSchemaMetaRow`	type
`NewNexusSchemaMetaRow`	type
`ErrorDefinition`	interface	A single entry in the unified error catalog.
`ProblemDetails`	interface	RFC 9457 Problem Details object. Structured error representation for API resp…
`ArchiveFields`	interface	Archive-specific fields for task upsert.
`RegisterAgentOptions`	interface	Options for registering a new agent instance.
`UpdateStatusOptions`	interface	Options for updating agent status.
`ListAgentFilters`	interface	Filters for listing agent instances.
`AgentHealthReport`	interface	Agent health report summary.
`AtomicMigrationResult`	interface	Atomic database migration result.
`ReleaseFn`	type	A release function returned by acquireLock.
`ProviderHookEvent`	type	CAAMP canonical hook event type. This is the normalized 16-event taxonomy fr…
`InternalHookEvent`	type
`HookEvent`	type	Full CLEO hook event union. CAAMP defines provider-facing canonical events;…
`HookPayload`	interface	Base interface for all hook payloads Provides common fields available across…
`SessionStartPayload`	interface	Payload for SessionStart hook (canonical: was onSessionStart) Fired when a CL…
`OnSessionStartPayload`	type
`SessionEndPayload`	interface	Payload for SessionEnd hook (canonical: was onSessionEnd) Fired when a CLEO s…
`OnSessionEndPayload`	type
`PreToolUsePayload`	interface	Payload for PreToolUse hook (canonical: was onToolStart) Fired when a task/to…
`OnToolStartPayload`	type
`PostToolUsePayload`	interface	Payload for PostToolUse hook (canonical: was onToolComplete) Fired when a tas…
`OnToolCompletePayload`	type
`HookHandler`	type	Handler function type for hook events Handlers receive project root and typed…
`HookRegistration`	interface	Hook registration metadata Tracks registered handlers with priority and event…
`HookConfig`	interface	Configuration for the hook system Controls which events are enabled/disabled
`NotificationPayload`	interface	Payload for Notification hook (canonical: was onFileChange) Fired when a trac…
`OnFileChangePayload`	type
`PostToolUseFailurePayload`	interface	Payload for PostToolUseFailure hook (canonical: was onError) Fired when an op…
`OnErrorPayload`	type
`PromptSubmitPayload`	interface	Payload for PromptSubmit hook (canonical: was onPromptSubmit) Fired when an a…
`OnPromptSubmitPayload`	type
`ResponseCompletePayload`	interface	Payload for ResponseComplete hook (canonical: was onResponseComplete) Fired w…
`OnResponseCompletePayload`	type
`SubagentStartPayload`	interface	Payload for SubagentStart hook Fired when a subagent process is launched
`SubagentStopPayload`	interface	Payload for SubagentStop hook Fired when a subagent process completes
`PreCompactPayload`	interface	Payload for PreCompact hook Fired before context compaction begins
`PostCompactPayload`	interface	Payload for PostCompact hook Fired after context compaction completes
`ConfigChangePayload`	interface	Payload for ConfigChange hook Fired when configuration is updated
`OnWorkAvailablePayload`	interface	Payload for onWorkAvailable hook Fired when the system detects ready work on…
`OnAgentSpawnPayload`	interface	Payload for onAgentSpawn hook Fired when a worker session/process is launched
`OnAgentCompletePayload`	interface	Payload for onAgentComplete hook Fired when a worker finishes its assigned run
`OnCascadeStartPayload`	interface	Payload for onCascadeStart hook Fired when autonomous execution begins flowin…
`OnPatrolPayload`	interface	Payload for onPatrol hook Fired when a watcher performs a periodic health/swe…
`CLEOLifecycleEvent`	type	Type for CLEO lifecycle event names These are the internal events CLEO fires…
`CLEOAutonomousLifecycleEvent`	type	Type for autonomous CLEO lifecycle events.
`SaveJsonOptions`	interface	Options for saveJson.
`CheckpointConfig`	interface	Checkpoint configuration.
`CheckpointStatus`	interface	Checkpoint status information.
`ChangedFile`	interface	Changed file with its status.
`SafetyOptions`	interface	Safety configuration - can be overridden per-operation
`RepairResult`	interface	Repair result with proper typing.
`SafetyConfig`	interface	Safety configuration options.
`NextDirectives`	type	Map of follow-up operation names to CLI command strings.
`TaskDetail`	interface	Enriched task with hierarchy info.
`PaginateInput`	interface	Input parameters for paginating a result set. T4668 T4663
`CompactTask`	interface	Compact task representation — minimal fields for list responses.
`ListTasksOptions`	interface	Filter options for listing tasks.
`ListTasksResult`	interface	Result of listing tasks.
`FindResult`	interface	Minimal task info for search results.
`FindTasksOptions`	interface	Options for finding tasks.
`FindTasksResult`	interface	Result of finding tasks.
`AdrFrontmatter`	interface	Parsed ADR frontmatter from .md file
`AdrRecord`	interface
`AdrSyncResult`	interface
`AdrListResult`	interface
`AdrFindResult`	interface
`PipelineAdrLinkResult`	interface
`EvidenceType`	type
`EvidenceRecord`	interface
`RelatedLink`	interface	Related link in frontmatter.
`FrontmatterMetadata`	interface	Frontmatter metadata for an RCASD artifact.
`ParsedFrontmatter`	interface	Result of parsing frontmatter from a markdown file.
`Stage`	type	Stage type derived from canonical stage list. T4800
`StageCategory`	type	Stage category for grouping related stages. T4800
`StageDefinition`	interface	Stage metadata with descriptive information. T4800
`TransitionRule`	interface	Transition rule - defines if a transition is allowed. T4800
`StageArtifactResult`	interface
`SkillFrontmatter`	interface	Skill frontmatter parsed from SKILL.md YAML header. This is CLEO’s extended…
`Skill`	interface	Skill definition loaded from disk. CLEO-specific type that wraps a…
`SkillSummary`	interface	Lightweight skill summary for manifest/listing. Projected from `Skill` for e…
`SkillManifest`	interface	Skill manifest (cached aggregate of all discovered skills).
`SkillProtocolType`	type	RCASD-IVTR+C protocol types.
`AgentConfig`	interface	Agent configuration from AGENT.md or agent definition.
`AgentRegistryEntry`	interface	Agent registry entry.
`AgentRegistry`	interface	Agent registry (persisted).
`SkillSearchScope`	type	CAAMP search order for skill discovery.
`SkillSearchPath`	interface	Ordered search path entry.
`DispatchStrategy`	type	Dispatch strategy for skill selection.
`DispatchResult`	interface	Dispatch result from skill_auto_dispatch.
`TokenDefinition`	interface	Token definition from placeholders.json.
`TokenValidationResult`	interface	Token validation result.
`TokenContext`	interface	Token injection context.
`OrchestratorThresholds`	interface	Orchestrator context thresholds.
`PreSpawnCheckResult`	interface	Pre-spawn check result.
`SpawnPromptResult`	interface	Spawn prompt result.
`DependencyWave`	interface	Dependency wave for parallel execution.
`DependencyAnalysis`	interface	Dependency analysis result.
`HitlSummary`	interface	HITL summary for session handoff.
`ManifestEntry`	interface	Research manifest entry (pipeline_manifest table, ADR-027).
`ManifestValidationResult`	interface	Manifest validation result.
`ComplianceResult`	interface	Compliance verification result.
`InstalledSkill`	interface	Installed skill tracking.
`InstalledSkillsFile`	interface	Installed skills file.
`TokenValues`	type	Token values map: TOKEN_NAME - value.
`MultiSkillComposition`	interface	Result of multi-skill composition.
`StageGuidance`	interface	Structured guidance for a single pipeline stage. Pi extensions consume the…
`EnforcementMode`	type	Lifecycle enforcement modes.
`GateData`	interface	Gate data within a stage.
`ManifestStageData`	interface	Stage data in an on-disk manifest.
`RcasdManifest`	interface	Canonical RCASD manifest-shaped interface for compatibility payloads. Lifecyc…
`GateCheckResult`	interface	Gate check result.
`StageTransitionResult`	interface	Stage transition result.
`LifecycleHistoryEntry`	interface	History entry for stage transitions.
`AlertLevel`	type	Alert level names.
`AlertCheckResult`	interface	Alert result from check_context_alert.
`FormatOptions`	interface	Options for envelope formatting. T4668 T4670 T4663
`CleoRegistryEntry`	interface	Entry in the CLEO-to-LAFS error registry. T4671 T4663
`TestDbEnv`	interface	Result of creating a test database environment.
`HierarchyValidation`	interface	Validate that adding a child to a parent would not violate constraints.
`TaskTreeNode`	interface	Build a tree structure from flat task list.
`HierarchyPolicy`	interface
`HierarchyValidationResult`	interface
`StrictnessPreset`	type	Valid preset names.
`PresetDefinition`	interface	A preset definition: the config keys it sets and a human description.
`ApplyPresetResult`	interface	Result of applying a preset.
`SessionRecord`	interface	Session object (engine-compatible).
`TaskWorkStateExt`	interface	Task work state from the task store. Extends the strict contracts…
`DecisionRecord`	interface	Decision record stored in decisions.jsonl.
`AssumptionRecord`	interface	Assumption record stored in assumptions.jsonl.
`RecordDecisionParams`	interface
`DecisionLogParams`	interface
`HandoffData`	interface	Handoff data schema - structured state for session transition.
`ComputeHandoffOptions`	interface	Options for computing handoff data.
`GitState`	interface	Git state snapshot captured at session end.
`DebriefDecision`	interface	Decision summary for debrief output.
`DebriefData`	interface	Rich debrief data — superset of HandoffData. Captures comprehensive session s…
`ComputeDebriefOptions`	interface	Options for computing debrief data.
`BrainFtsRow`	interface	Row returned by FTS content_hash duplicate check (brain-retrieval.ts observeB…
`BrainNarrativeRow`	interface	Row returned by narrative backfill query (brain-retrieval.ts populateEmbeddin…
`BrainSearchHit`	interface	Flattened FTS hit used in hybrid search scoring (brain-search.ts hybridSearch).
`BrainKnnRow`	interface	Row returned by KNN vector similarity query (brain-similarity.ts searchSimilar).
`BrainDecisionNode`	interface	Decision node attached to a blocker in causal traces (brain-reasoning.ts reas…
`BrainAnchor`	interface	Anchor entry in a timeline result (brain-retrieval.ts timelineBrain).
`BrainTimelineNeighborRow`	interface	Row returned by timeline UNION ALL neighbor queries (brain-retrieval.ts timel…
`BrainConsolidationObservationRow`	interface	Row returned by the consolidation observation query (brain-lifecycle.ts conso…
`BrainIdCheckRow`	interface	Row returned by ID existence check queries (claude-mem-migration.ts). Used b…
`EmbeddingProvider`	interface	Contract for embedding providers (local models, API services, etc.).
`SimilarityResult`	interface
`BrainSearchResult`	interface	Search result with BM25 rank.
`BrainSearchOptions`	interface	Search options.
`HybridResult`	interface	Result from hybridSearch combining multiple search signals.
`HybridSearchOptions`	interface	Options for hybridSearch weighting and limits.
`MemoryBridgeConfig`	interface	Configuration for memory bridge content generation.
`BrainCompactHit`	interface	Compact search hit — minimal fields for index-level results.
`SearchBrainCompactParams`	interface	Parameters for searchBrainCompact.
`SearchBrainCompactResult`	interface	Result from searchBrainCompact.
`TimelineBrainParams`	interface	Parameters for timelineBrain.
`TimelineNeighbor`	interface	Timeline entry — compact id/type/date tuple.
`TimelineBrainResult`	interface	Result from timelineBrain.
`FetchBrainEntriesParams`	interface	Parameters for fetchBrainEntries.
`FetchedBrainEntry`	interface	Fetched entry with full data.
`FetchBrainEntriesResult`	interface	Result from fetchBrainEntries.
`BrainObservationType`	type	Observation type from schema.
`BrainObservationSourceType`	type	Observation source type from schema.
`ObserveBrainParams`	interface	Parameters for observeBrain.
`ObserveBrainResult`	interface	Result from observeBrain.
`PopulateEmbeddingsResult`	interface	Result from populateEmbeddings backfill.
`PopulateEmbeddingsOptions`	interface	Options for the embedding backfill pipeline.
`AuditEntry`	interface	Audit entry interface. Used by session-grade and system-engine for behavioral…
`StoreLearningParams`	interface	Parameters for storing a new learning.
`SearchLearningParams`	interface	Parameters for searching learnings.
`DimensionScore`	interface
`GradeResult`	interface
`AdapterInfo`	interface	Summary info for an adapter without exposing the full instance.
`SessionBridgeData`	interface	Session data needed to create a memory bridge observation.
`StoreDecisionParams`	interface	Parameters for storing a new decision.
`SearchDecisionParams`	interface	Parameters for searching decisions.
`ListDecisionParams`	interface	Parameters for listing decisions.
`PatternType`	type	Pattern types from ADR-009.
`PatternImpact`	type	Impact level.
`StorePatternParams`	interface	Parameters for storing a new pattern.
`SearchPatternParams`	interface	Parameters for searching patterns.
`RecordAssumptionParams`	interface
`BulkLinkEntry`	interface	A link to be created in bulk.
`SessionMemoryResult`	interface	Result of persisting session memory to brain.db.
`MemoryItem`	interface	A memory item to be persisted to brain.db.
`SessionMemoryContext`	interface	Memory context returned for session start/resume enrichment.
`Pipeline`	interface	Pipeline entity representing a task’s lifecycle state. T4800 T4799 - Unifi…
`PipelineStageRecord`	interface	Pipeline stage record linking pipeline to individual stages. T4800 T4801 -…
`PipelineTransition`	interface	Pipeline transition record for audit trail. T4800 T4801 - Requires pipelin…
`InitializePipelineOptions`	interface	Options for initializing a pipeline. T4800
`AdvanceStageOptions`	interface	Options for advancing pipeline stage. T4800
`PipelineQueryOptions`	interface	Pipeline query options. T4800
`BriefingTask`	interface	Task summary for briefing output.
`BriefingBug`	interface	Bug summary for briefing output.
`BriefingBlockedTask`	interface	Blocked task summary for briefing output.
`BriefingEpic`	interface	Active epic summary for briefing output.
`PipelineStageInfo`	interface	Pipeline stage data for briefing output.
`LastSessionInfo`	interface	Last session info with handoff data.
`CurrentTaskInfo`	interface	Currently active task info.
`SessionBriefing`	interface	Session briefing result.
`BriefingOptions`	interface	Options for computing session briefing.
`MinimalSessionRecord`	interface	Minimal session record returned by findSessions().
`FindSessionsParams`	interface	Parameters for findSessions().
`ContextDriftResult`	interface
`SessionHistoryEntry`	interface
`SessionHistoryParams`	interface
`SessionStatsResult`	interface
`RuntimeProviderContext`	interface
`RuntimeProviderSnapshot`	interface
`StartSessionOptions`	interface	Options for starting a session.
`EndSessionOptions`	interface	Options for ending a session.
`ListSessionsOptions`	interface	Options for listing sessions.
`EnforcementMode`	type	Enforcement modes.
`ActiveSessionInfo`	interface	Session info for enforcement checks.
`EnforcementResult`	interface	Enforcement result.
`ValidationResult`	interface
`AddTaskEnforcementOptions`	interface
`UpdateTaskEnforcementOptions`	interface
`AcceptanceEnforcement`	interface
`ResolvedParent`	interface	Minimal parent task shape needed for pipeline stage resolution. T060
`TaskPipelineStage`	type	Union type of all valid pipeline stage names.
`LifecycleMode`	type	The resolved enforcement mode (from lifecycle.mode config key).
`EpicEnforcementResult`	interface	Result of an enforcement check. `warning` is populated in advisory mode.
`AddTaskOptions`	interface	Options for creating a task. `description` is required per CLEO’s anti-h…
`AddTaskResult`	interface	Result of adding a task.
`ListPhasesResult`	interface	Options for listing phases.
`SetPhaseOptions`	interface	Options for setting current phase.
`SetPhaseResult`	interface	Result of a phase set operation.
`ShowPhaseResult`	interface	Phase show result.
`AdvancePhaseResult`	interface	Phase advance result.
`RenamePhaseResult`	interface	Phase rename result.
`DeletePhaseResult`	interface	Phase delete result.
`PruneResult`	interface
`SchemaInstallResult`	interface
`StalenessReport`	interface
`InstalledSchema`	interface
`CheckResult`	interface
`JsonFileIntegrityResult`	interface	Result for a single file check.
`SchemaIntegrityReport`	interface	Full integrity report for all JSON files.
`ProjectType`	type	Detected project type.
`TestFramework`	type	Test framework.
`FileNamingConvention`	type
`ImportStyle`	type
`ProjectContext`	interface	Schema-compliant project context for LLM agent consumption.
`ScaffoldResult`	interface
`InjectionCheckResult`	interface
`ScaffoldResult`	interface	Result of an ensure* scaffolding operation.
`CheckStatus`	type	Status of a check* diagnostic.
`CheckResult`	interface	Result of a check* diagnostic (compatible with doctor/checks.ts CheckResult).
`ProjectClassification`	interface	Classification result for a project directory.
`ClassificationSignal`	interface	A single classification signal detected on the filesystem.
`ScaffoldResult`	interface
`HookCheckResult`	interface
`EnsureGitHooksOptions`	interface
`ManagedHook`	type
`LegacyDetectionResult`	interface	Result of detecting legacy agent-output directories.
`AgentOutputsMigrationResult`	interface	Result of running the agent-outputs migration.
`NexusPermissionLevel`	type
`NexusHealthStatus`	type
`NexusProject`	interface	Domain representation of a registered Nexus project.
`NexusRegistryFile`	interface	Legacy registry file shape (pre-SQLite). Retained for migration compatibility.
`StackAnalysis`	interface
`ArchAnalysis`	interface
`StructureAnalysis`	interface
`ConventionAnalysis`	interface
`TestingAnalysis`	interface
`IntegrationAnalysis`	interface
`ConcernAnalysis`	interface
`CodebaseMapResult`	interface
`MapCodebaseOptions`	interface
`InitOptions`	interface	Options for the init operation.
`InitResult`	interface	Result of the init operation.
`BootstrapContext`	interface	Result tracking arrays passed through each bootstrap step.
`BootstrapOptions`	interface	Options for bootstrapGlobalCleo.
`ExportFormat`	type
`ExportParams`	interface
`ExportResult`	interface
`ImportParams`	interface
`ImportResult`	interface
`AgentExecutionOutcome`	type	The outcome of an agent’s execution attempt on a task.
`AgentExecutionEvent`	interface	Context recorded when an agent completes or fails a task.
`AgentPerformanceSummary`	interface	Summary of an agent type’s execution performance on a task type.
`HealingSuggestion`	interface	A self-healing suggestion derived from failure pattern history.
`AgentCapacity`	interface	Task-count-based capacity for a single agent instance.
`AgentPerformanceMetrics`	interface	Metrics provided when recording agent performance.
`CapacitySummary`	interface	Capacity summary for reporting.
`AgentHealthStatus`	interface	Health status of a specific agent instance.
`RetryPolicy`	interface	Configuration for retry behavior.
`RetryResult`	interface	Result of a retried operation.
`AgentRecoveryResult`	interface	Result of a recovery attempt for a single agent.
`RiskFactor`	interface	A single factor contributing to a task’s overall risk score. Each factor has…
`RiskAssessment`	interface	Complete risk assessment for a single task. Returned by `calculateTaskRisk`…
`ValidationPrediction`	interface	Predicted outcome for a lifecycle validation gate. Returned by…
`DetectedPattern`	interface	A pattern automatically detected from historical brain/task data. Detected p…
`PatternMatch`	interface	Result of matching a task against known patterns from brain_patterns. Includ…
`PatternExtractionOptions`	interface	Options for pattern extraction from historical data.
`PatternStatsUpdate`	interface	Result of updating pattern statistics after an outcome.
`LearningContext`	interface	Summary of applicable learnings for a task, used in prediction.
`ImpactAssessment`	interface	Full impact assessment for a task within its dependency graph. Captures dire…
`ChangeType`	type	The type of change being analyzed.
`ChangeImpact`	interface	Predicted downstream effects of a specific change to a task. Models what hap…
`AffectedTask`	interface	A single task affected by a change, with its predicted new state.
`ImpactedTask`	interface	A single task predicted to be affected by a free-text change description. Pr…
`ImpactReport`	interface	Full impact prediction report for a free-text change description. Returned b…
`BlastRadiusSeverity`	type	Severity classification for blast radius.
`BlastRadius`	interface	Quantified scope of a task’s impact across the project.
`GateFocusRecommendation`	interface	A gate-level focus recommendation produced by adaptive validation.
`AdaptiveValidationSuggestion`	interface	Full adaptive validation suggestion set for a task.
`VerificationConfidenceScore`	interface	Result of scoring and persisting a completed verification round.
`StorePredictionOptions`	interface	Parameters for storing a quality prediction as a brain observation.
`DependencyCheckResult`	interface	Result of a dependency validation check.
`DependencyError`	interface	A dependency error.
`DependencyWarning`	interface	A dependency warning.
`DependencyWave`	interface	A wave of parallelizable tasks.
`NexusParsedQuery`	interface
`NexusResolvedTask`	type	Task with project context annotation.
`DiscoverResult`	interface
`NexusDiscoverResult`	interface
`SearchResult`	interface
`NexusSearchResult`	interface
`PermissionCheckResult`	interface
`SharingStatus`	interface	Result of a sharing status check.
`TaskCurrentResult`	interface	Result of getting current task.
`TaskStartResult`	interface	Result of starting work on a task.
`TaskWorkHistoryEntry`	interface	Task work history entry.
`CompleteTaskOptions`	interface	Options for completing a task.
`CompleteTaskResult`	interface	Result of completing a task.
`RuleViolation`	interface	Validation error from anti-hallucination checks
`UpdateTaskOptions`	interface	Options for updating a task.
`UpdateTaskResult`	interface	Result of updating a task.
`ParsedDirective`	interface	Parsed directive from a Conduit message.
`RouteResult`	interface	Result of routing a directive to a project.
`WorkspaceStatus`	interface	Aggregated task status across all projects.
`WorkspaceProjectSummary`	interface	Task summary for a single project.
`WorkspaceAgent`	interface	Agent info aggregated across projects.
`ProjectACL`	interface	Project-level ACL entry.
`DepNode`	interface	A node in the dependency graph.
`DepsOverviewResult`	interface	Dependency overview result.
`TaskDepsResult`	interface	Single task dependency result.
`ExecutionWave`	interface	Execution wave (group of parallelizable tasks).
`CriticalPathResult`	interface	Critical path result.
`CycleResult`	interface	Cycle detection result.
`TreeNode`	interface	Tree node representation.
`CircularDependency`	type	A circular dependency cycle found via DFS traversal.
`MissingDependency`	interface	A missing dependency reference within an epic.
`DependencyAnalysis`	interface	Full dependency analysis result for an epic.
`ContextEstimation`	interface	Context estimation result.
`Wave`	interface
`EnrichedWave`	interface
`StatusCounts`	interface	Status counts by task state.
`EpicStatus`	interface	Epic-specific status result.
`OverallStatus`	interface	Overall orchestration status (no specific epic).
`ProgressMetrics`	interface	Progress metrics for orchestration check.
`StartupSummary`	interface	Startup summary for an epic.
`OrchestratorSession`	interface	Orchestrator session state.
`SpawnContext`	interface	Spawn context for a subagent.
`TaskReadiness`	interface	Task readiness assessment.
`AnalysisResult`	interface	Orchestrator analysis result.
`ArtifactType`	type	Supported artifact types.
`ArtifactConfig`	interface	Artifact configuration from release config.
`ArtifactResult`	interface	Result of an artifact operation.
`ArtifactHandler`	interface	Artifact handler interface.
`ReleaseConfig`	interface	Release configuration shape.
`ReleaseGate`	interface	Release gate definition.
`GitFlowConfig`	interface	GitFlow branch configuration.
`ChannelConfig`	interface	Channel-to-branch mapping for npm dist-tag resolution.
`PushMode`	type	Push mode: direct push vs PR creation vs auto-detect.
`ReleaseChannel`	type	npm dist-tag channel for a release.
`ChannelValidationResult`	interface	Result of validating a version string against a channel’s expectations.
`CIPlatform`	type	Supported CI/CD platforms.
`BranchProtectionResult`	interface
`PRCreateOptions`	interface
`PRResult`	interface
`RepoIdentity`	interface
`EpicCompletenessResult`	interface	Epic completeness result.
`DoubleListingResult`	interface	Double-listing check result.
`BumpType`	type	Bump type for version calculation.
`VersionBumpTarget`	interface	Version bump target config from .cleo/config.json.
`BumpResult`	interface	Bump result for a single file.
`ReleaseManifest`	interface	Release manifest structure.
`ReleaseListOptions`	interface
`ReleaseTaskRecord`	interface	Task record shape needed for release operations.
`ReleaseGateMetadata`	interface	Metadata captured during gate evaluation, returned alongside gate results. Do…
`PushPolicy`	interface	Push policy configuration from config.release.push.
`SnapshotDecision`	interface	A decision recorded during the session.
`SnapshotObservation`	interface	Brain observation linked to this session.
`SnapshotTaskContext`	interface	Active task context at snapshot time.
`SessionSnapshot`	interface	Complete session snapshot — everything needed to resume. This is the seriali…
`SerializeOptions`	interface	Options for serializing a session.
`RestoreOptions`	interface	Options for restoring a session.
`StickyNoteStatus`	type	Sticky note status values.
`StickyNoteColor`	type	Sticky note color options.
`StickyNotePriority`	type	Sticky note priority levels.
`ConvertedTargetType`	type	Converted target type.
`ConvertedTarget`	interface	Converted target reference.
`StickyNote`	interface	Core sticky note interface.
`CreateStickyParams`	interface	Parameters for creating a sticky note.
`ListStickiesParams`	interface	Parameters for listing sticky notes.
`ConvertStickyParams`	interface	Parameters for converting a sticky note.
`ArchiveTasksOptions`	interface	Options for archiving tasks.
`ArchiveTasksResult`	interface	Result of archiving tasks.
`DeleteTaskOptions`	interface	Options for deleting a task.
`DeleteTaskResult`	interface	Result of deleting a task.
`EngineResult`	interface	Canonical EngineResult type used by all engines and core engine-compat modules.
`ExportMeta`	interface	Export package metadata.
`ExportSelection`	interface	Export selection criteria.
`IdMapEntry`	interface	ID map entry.
`RelationshipGraph`	interface	Relationship graph.
`ExportPackage`	interface	Complete export package.
`ExportTasksParams`	interface
`ExportTasksResult`	interface
`HelpOperationDef`	interface	Minimal operation definition consumed by help logic.
`CostHint`	type	Cost hint classification for an operation.
`GroupedOperations`	interface	Domain-grouped operation format (compact).
`VerboseOperation`	interface	Verbose operation entry with cost hints.
`HelpResult`	interface	Result of the help computation.
`TransferMode`	type	Transfer mode: copy keeps source tasks, move archives them.
`TransferScope`	type	Transfer scope: single task or full subtree.
`TransferOnConflict`	type	Conflict resolution when target has tasks with duplicate titles.
`TransferOnMissingDep`	type	How to handle missing dependencies in the target project.
`TransferParams`	interface	Parameters for a cross-project transfer operation.
`TransferManifestEntry`	interface	A single task entry in the transfer manifest.
`TransferManifest`	interface	Manifest describing what was (or would be) transferred.
`TransferResult`	interface	Result of a transfer operation.
`ImportFromPackageOptions`	interface	Options passed to importFromPackage (extracted from importTasksPackage).
`ImportFromPackageResult`	interface	Result from importFromPackage.
`RemapTable`	interface	Forward and reverse remap tables.
`ImportTasksParams`	interface
`ImportTasksResult`	interface
`ValidationError`	interface
`ValidationResult`	interface
`AdrValidationError`	type	ValidationError — canonical name per ADR-017 spec
`AdrValidationResult`	type	ValidationResult — canonical name per ADR-017 spec
`TreeSitterLanguage`	type	Supported tree-sitter language identifiers.
`OutlineNode`	interface	A symbol node in the outline tree, with optional children.
`SmartOutlineResult`	interface	Result of generating a smart outline for a file.
`SmartSearchResult`	interface	A search result with relevance score.
`SmartSearchOptions`	interface	Options for smart_search.
`SmartUnfoldResult`	interface	Result of unfolding a single symbol.
`ComplianceJsonlEntry`	type
`PayloadValidationResult`	interface	Result of payload validation.
`BuildConfig`	type
`RepositoryConfig`	type
`IssueTemplate`	interface	Parsed issue template.
`AddIssueParams`	interface
`AddIssueResult`	interface
`RetryablePredicate`	type	A predicate or pattern used to decide whether an error is retryable. -…
`RetryOptions`	interface	Options that control retry behavior for `withRetry`.
`RetryContext`	interface	Metadata attached to errors thrown after all retry attempts are exhausted. T…
`DecayResult`	interface	Result from applying temporal decay.
`ConsolidationResult`	interface	Result from consolidating memories.
`BrainMigrationResult`	interface	Result from a migration run.
`ResearchEntry`	interface	Research entry attached to a task.
`ManifestEntry`	interface	Manifest entry (JSONL line).
`AddResearchOptions`	interface	Options for adding research.
`ListResearchOptions`	interface	Options for listing research.
`ManifestQueryOptions`	interface	Manifest query options.
`ExtendedManifestEntry`	interface	Extended manifest entry with optional fields used by the engine.
`ResearchFilter`	interface	Research filter criteria used by the engine.
`ContradictionDetail`	interface	Contradiction detail between two manifest entries.
`SupersededDetail`	interface	Superseded entry detail.
`ComplianceSummary`	interface	Compliance summary shape.
`OtelCaptureMode`	type	OTel capture mode.
`OtelTokenDataPoint`	interface	Token data point parsed from OTel metrics.
`AggregatedTokens`	interface	Aggregated token counts.
`ABVariant`	type	A/B test variant.
`ABEventType`	type	A/B test event types.
`ABTestSummary`	interface	A/B test summary result.
`Severity`	enum	Violation severity levels.
`ManifestIntegrity`	enum	Manifest integrity states.
`InstructionStability`	enum	Instruction stability levels.
`SessionDegradation`	enum	Session degradation levels.
`AgentReliability`	enum	Agent reliability levels.
`MetricCategory`	enum	Metric categories.
`MetricSource`	enum	Metric sources.
`AggregationPeriod`	enum	Aggregation periods.
`TokenEventType`	type	Token event types.
`TokenEvent`	interface	A token usage event entry.
`TokenSessionSummary`	interface	Token session summary shape.
`VerificationResult`	interface	Result of a backup verification operation.
`LogLevel`	type	Log entry severity level
`MigrationLogEntry`	interface	Single migration log entry
`MigrationLoggerConfig`	interface	Migration logger configuration
`PreflightResult`	interface	Pre-flight check result.
`MigrationPhase`	type	Migration phase - tracks current step in the migration process
`SourceFileInfo`	interface	Source file info with checksum for integrity verification
`MigrationProgress`	interface	Migration progress tracking
`MigrationState`	interface	Complete migration state structure
`JsonFileValidation`	interface	Result of validating a single JSON file.
`JsonValidationResult`	interface	Complete validation result for all source files.
`SchemaVersion`	interface	Schema version info.
`MigrationFn`	type	Migration function signature.
`MigrationDef`	interface	Migration definition.
`MigrationResult`	interface	Migration run result.
`MigrationStatus`	interface	Status of all data files.
`NexusGraphNode`	interface
`NexusGraphEdge`	interface
`NexusGlobalGraph`	interface
`DepsResult`	interface	Result of a dependency query.
`DepsEntry`	interface	Single dependency entry with resolution status.
`CriticalPathResult`	interface	Critical path result.
`BlockingAnalysisResult`	interface	Blocking analysis result.
`OrphanEntry`	interface	Orphan detection result.
`PinoLevel`	type	Pino log levels as written by CLEO’s logger (uppercase).
`PinoLogEntry`	interface	A parsed pino log entry from a CLEO log file. Core fields are always present;…
`LogFileInfo`	interface	Metadata about a discovered log file.
`LogFilter`	interface	Filter criteria for log queries. All fields are optional; when multiple are p…
`LogQueryResult`	interface	Result of a log query operation.
`LogDiscoveryOptions`	interface	Options for discovering log files.
`LogSummary`	interface	Summary of log activity across files.
`RemoteConfig`	interface	Remote configuration.
`PushResult`	interface	Result of a push operation.
`PullResult`	interface	Result of a pull operation.
`RemoteInfo`	interface	Result of a remote list operation.
`ExecutionMode`	type	Execution mode for an operation
`GatewayType`	type	Gateway type
`PreferredChannel`	type	Preferred communication channel for token efficiency. CLI is the only dispatc…
`OperationCapability`	interface
`CapabilityReport`	interface	Capability report returned by system.doctor
`RateLimitConfig`	interface	Rate limiter configuration
`RateLimitResult`	interface	Rate limit check result
`ContributionDecision`	interface	A contribution decision from an agent.
`ContributionConflict`	interface	Conflict between two agent decisions.
`ConsensusResult`	interface	Consensus result from weighted voting.
`SkillsMpConfig`	interface	SkillsMP configuration.
`MarketplaceSkill`	interface	Marketplace skill result (CLEO-specific shape).
`BatchSpawnEntry`	interface	Result of a single spawn within a batch.
`BatchSpawnResult`	interface	Result of a batch spawn operation.
`SessionInitResult`	interface	Session init result.
`PauseStatus`	interface	Pause status result.
`SkillSourceType`	type	Source type classification for a skill directory.
`SkillSourceMode`	type	Skill source mode.
`SkillSearchPath`	interface	Search path entry with its origin.
`IssueSeverity`	type	Validation issue severity.
`ValidationIssue`	interface	Single validation issue.
`SkillValidationResult`	interface	Validation result for a skill.
`SnapshotMeta`	interface	Snapshot metadata.
`SnapshotTask`	interface	Portable task representation (subset of Task, omitting local-only fields).
`Snapshot`	interface	Complete snapshot package.
`ImportResult`	interface	Import result summary.
`SpawnCapability`	type	Spawn capability type - subset of provider capabilities related to spawning
`WorkflowRuleMetric`	interface	Per-rule compliance breakdown.
`WorkflowComplianceReport`	interface	Full workflow compliance report.
`ArchiveMetadata`	interface	Archive metadata that may be attached to archived task records.
`AnalyticsTask`	interface	Archived task shape used internally for analytics.
`ArchiveReportType`	type
`SummaryReportData`	interface	Summary report result.
`PhaseGroupEntry`	interface	Phase group entry.
`LabelFrequencyEntry`	interface	Label frequency entry.
`PriorityGroupEntry`	interface	Priority group entry.
`CycleTimeDistribution`	interface	Cycle time distribution buckets.
`CycleTimePercentiles`	interface	Cycle time percentiles.
`CycleTimesReportData`	interface	Cycle times report result.
`DailyArchiveEntry`	interface	Daily archive entry.
`MonthlyArchiveEntry`	interface	Monthly archive entry.
`TrendsReportData`	interface	Trends report result.
`EmptyArchiveData`	interface	Empty archive sentinel (when totalArchived is 0).
`ArchiveReportDataMap`	type	Union type mapping report types to their data shapes.
`ArchiveAnalyticsResult`	interface	The envelope returned by analyzeArchive.
`AnalyzeArchiveOptions`	interface	Options for analyzeArchive.
`ArchiveStatsResult`	interface
`AuditIssue`	interface
`AuditResult`	interface
`BackupResult`	interface
`RestoreResult`	interface
`BackupEntry`	interface	A single backup entry returned by listSystemBackups.
`CleanupResult`	interface
`Platform`	type	Detected platform.
`SystemInfo`	interface	Structured snapshot of the host system for diagnostics, error reports, and lo…
`CheckStatus`	type
`CheckResult`	interface
`HealthCheck`	interface
`HealthResult`	interface
`DiagnosticsCheck`	interface
`DiagnosticsResult`	interface
`DoctorCheck`	interface
`DoctorReport`	interface
`FixResult`	interface
`StartupState`	type	Outcome of a startup health check. Tells the caller exactly what state the sy…
`StartupHealthCheck`	interface
`StartupHealthResult`	interface
`InjectGenerateResult`	interface
`LabelsResult`	interface
`SystemMetricsResult`	interface
`MigrateResult`	interface
`RuntimeDiagnostics`	interface
`SafestopResult`	interface
`UncancelResult`	interface
`TemplateSection`	interface	A single section/field within an issue template.
`IssueTemplate`	interface	A parsed issue template.
`TemplateConfig`	interface	The full template config output.
`TemplateResult`	interface	Result type for template parser operations.
`ShellType`	type	Supported shell types.
`ChangelogSection`	interface	Grouped changelog sections.
`CommandMeta`	interface	Parsed command metadata.
`ParsedFlags`	interface	Parsed flag state.
`InsertTask`	type
`SelectTask`	type
`InsertTaskDependency`	type
`SelectTaskDependency`	type
`InsertTaskRelation`	type
`SelectTaskRelation`	type
`InsertSession`	type
`SelectSession`	type
`InsertWorkHistory`	type
`SelectWorkHistory`	type
`InsertLifecyclePipeline`	type
`SelectLifecyclePipeline`	type
`InsertLifecycleStage`	type
`SelectLifecycleStage`	type
`InsertLifecycleGateResult`	type
`SelectLifecycleGateResult`	type
`InsertLifecycleEvidence`	type
`SelectLifecycleEvidence`	type
`InsertLifecycleTransition`	type
`SelectLifecycleTransition`	type
`InsertSchemaMeta`	type
`SelectSchemaMeta`	type
`InsertAuditLog`	type
`SelectAuditLog`	type
`AuditLogInsert`	type	Canonical type alias for audit log insert (T4848).
`AuditLogSelect`	type	Canonical type alias for audit log select (T4848).
`InsertTokenUsage`	type
`SelectTokenUsage`	type
`InsertArchitectureDecision`	type
`SelectArchitectureDecision`	type
`InsertManifestEntry`	type
`SelectManifestEntry`	type
`InsertPipelineManifest`	type
`SelectPipelineManifest`	type
`InsertReleaseManifest`	type
`SelectReleaseManifest`	type
`InsertExternalTaskLink`	type
`SelectExternalTaskLink`	type
`InsertAgentInstance`	type
`SelectAgentInstance`	type
`InsertAgentErrorLog`	type
`SelectAgentErrorLog`	type
`ManifestIntegrity`	type
`Severity`	type
`ComplianceMetrics`	interface
`ManifestEntry`	interface
`TokenMetrics`	interface
`TokenEfficiency`	interface
`OrchestrationOverhead`	interface
`DriftIssue`	interface
`DriftReport`	interface
`CommandIndexEntry`	interface
`CommandIndex`	interface
`SchemaVersions`	interface
`FileHashes`	interface
`ProjectCacheEntry`	interface
`DoctorProjectCache`	interface
`ProjectDetail`	interface
`CategorizedProjects`	interface
`UserJourneyStage`	type
`HealthSummary`	interface
`ValidationError`	interface
`ValidationResult`	interface
`Task`	interface
`TaskData`	interface	Task data shape for validation functions.
`ArchiveData`	interface	Archive data shape for validation functions.
`ComprehensiveValidationResult`	interface
`ManifestDoc`	interface
`GapEntry`	interface
`CoverageEntry`	interface
`GapReport`	interface
`ManifestEntry`	interface
`ManifestViolation`	interface
`ManifestValidationResult`	interface
`ComplianceEntry`	interface
`ProtocolViolation`	interface
`ProtocolValidationResult`	interface
`GateName`	type
`AgentName`	type
`FailureLogEntry`	interface
`VerificationGates`	interface
`Verification`	interface
`VerificationStatus`	type
`CircularValidationResult`	interface
`TaskForVerification`	interface
`ProjectInfo`	interface	Fields consumed by logging, audit, and correlation subsystems.
`BackfillOptions`	interface	Options for backfillTasks().
`BackfillTaskChange`	interface	Summary of what was (or would be) changed for a single task.
`BackfillResult`	interface	Overall result returned by backfillTasks().
`RequirementLevel`	type	RFC 2119 requirement levels
`ViolationSeverity`	type	Violation severity
`ProtocolRule`	interface	Protocol rule definition
`ProtocolViolation`	interface	Protocol violation result
`ProtocolValidationResult`	interface	Protocol validation result
`ErrorSeverity`	enum	Error severity levels for protocol/gate validation.
`ErrorCategory`	enum	Error category for grouping protocol/gate violations.
`ProtocolExitCode`	enum	Protocol-specific exit codes used by the RCASD-IVTR+C enforcement system. Th…
`ProtocolRequest`	interface	Request shape used by the protocol enforcement system. Minimal interface matc…
`ProtocolResponse`	interface	Response shape used by the protocol enforcement system.
`ProtocolType`	enum	Protocol types aligned with RCASD-IVTR+C lifecycle
`ViolationLogEntry`	interface	Violation log entry
`ChainFindCriteria`	interface
`ProtocolViolation`	interface	Protocol violation entry.
`ProtocolValidationResult`	interface	Protocol validation result.
`ManifestEntryInput`	interface	Manifest entry structure for validation.
`ProtocolType`	type
`VotingMatrix`	interface
`AdrStatus`	type	ADR lifecycle status values. T260
`ArchitectureDecisionOptions`	interface	Architecture decision options for validator.
`ValidationStageOptions`	interface	Validation-stage options for validator.
`TestFramework`	type	Project-agnostic test framework identifiers. The testing protocol is deliber…
`TestingOptions`	interface	Testing-stage options for validator.
`BrainMaintenanceDecayResult`	interface	Temporal decay step result subset used in maintenance output.
`BrainMaintenanceConsolidationResult`	interface	Memory consolidation step result subset used in maintenance output.
`BrainMaintenanceReconciliationResult`	interface	Orphaned reference reconciliation step result.
`BrainMaintenanceEmbeddingsResult`	interface	Embedding backfill step result.
`BrainMaintenanceResult`	interface	Aggregated result from a full brain maintenance run. All counts are zero whe…
`BrainMaintenanceOptions`	interface	Options for `runBrainMaintenance`. All `skip*` flags default to `false` — th…
`ClaudeMemMigrationResult`	interface	Result from a claude-mem migration run.
`ClaudeMemMigrationOptions`	interface	Options for the claude-mem migration.
`BlockerNode`	interface
`CausalTrace`	interface
`SimilarEntry`	interface
`ManifestEntry`	type
`ModelProviderLookup`	interface
`TokenMethod`	type
`TokenConfidence`	type
`TokenTransport`	type
`TokenExchangeInput`	interface
`TokenMeasurement`	interface
`TokenUsageFilters`	interface
`TokenUsageSummary`	interface
`SkillEntry`	interface
`SkillContent`	interface
`HighImpactTask`	interface
`SingleBlockerTask`	interface
`CommonBlocker`	interface
`UnblockResult`	interface
`ValidationIssue`	interface
`SpawnValidationResult`	interface
`ContextInjectionData`	interface	Data returned by context injection.
`CancelResult`	interface	Result of a cancel operation.
`FlatTreeNode`	interface	Tree node representation for task hierarchy.
`ComplexityFactor`	interface	Complexity factor contributing to a task’s size estimate.
`AnalysisResult`	interface
`StoreEngine`	type	Store engine type. SQLite is the only supported engine (ADR-006). T4647
`TaskFilters`	interface	Common task filter options.
`SessionFilters`	interface	Common session filter options.
`StoreProvider`	interface	Store provider interface. Backed by SQLite (ADR-006 canonical storage).
`MigrationResult`	interface	Migration result.
`MigrationOptions`	interface	Options for migration.
`RepairAction`	interface	A single repair action with status.
`UpgradeAction`	interface	A single upgrade action with status.
`UpgradeResult`	interface	Full upgrade result.
`UpgradeSummary`	interface	Counts of what upgrade checked/applied/skipped.
`DiagnoseFinding`	interface	A single diagnostic finding from —diagnose.
`DiagnoseResult`	interface	Result from diagnoseUpgrade().
`GateLayer`	enum	Gate layer enumeration
`GateStatus`	enum	Gate status for each layer
`GateViolation`	interface	Violation detail for a specific gate layer
`LayerResult`	interface	Result from a single gate layer validation
`VerificationResult`	interface	Complete verification result across all 4 layers
`OperationContext`	interface	Operation context for gate validation
`WorkflowGateName`	enum	Workflow gate names per protocol specification Section 7.1 T3141
`WorkflowGateStatus`	type	Workflow gate status values per Section 7.3
`WorkflowGateAgent`	type	Agent responsible for each gate per Section 7.2
`WorkflowGateDefinition`	interface	Individual workflow gate definition per Section 7.2
`WorkflowGateState`	interface	State of a single workflow gate
`JsonSchemaType`	type
`JsonSchemaProperty`	interface
`JSONSchemaObject`	interface
`CommanderArgSplit`	interface
`ValidationResult`	interface	Validation result
`ValidationError`	interface	Individual validation error
`SchemaType`	type	Schema types that can be validated via AJV/JSON Schema. SQLite-backed types (…
`ComplianceEntry`	interface	Compliance entry stored in COMPLIANCE.jsonl
`CoherenceIssue`	interface	Coherence issue found during graph validation.
`ValidateCheckDetail`	interface
`ValidateReportResult`	interface
`ValidateAndFixResult`	interface	Result from validate + fix operation.
`CriticalPathNode`	interface
`CriticalPathResult`	interface
`SkillsPrecedenceConfig`	interface	Configuration for skill precedence resolution across providers.
`ResolvedSkillPath`	interface	A resolved skill path with full provenance metadata.
`SkillInstallationContext`	interface	Context for a skill installation operation.
`InProgressEpic`	interface	In-progress epic entry.
`ReadyTask`	interface	Ready task entry with leverage analysis.
`BlockedTask`	interface	Blocked task entry.
`OpenBug`	interface	Open bug entry.
`PlanMetrics`	interface	Planning metrics.
`PlanResult`	interface	Composite planning view result.
`RcasdIndex`	interface	RCASD-INDEX.json top-level structure.
`IndexMeta`	interface	Index metadata.
`IndexTotals`	interface	Aggregate counts.
`TaskAnchor`	interface	Task-anchored RCASD artifact reference.
`SpecEntry`	interface	Specification entry.
`ReportEntry`	interface	Report entry.
`PipelineState`	interface	Pipeline state.
`PipelineOperation`	interface	Active pipeline operation.
`ChangeEntry`	interface	Change entry.
`ExecutionResult`	interface	The aggregate result of executing a CANT workflow.
`StepResult`	interface	The result of a single workflow statement execution.
`DiscretionContext`	interface	Context provided to a discretion evaluator for AI-judged conditions.
`ApprovalTokenStatus`	type	Valid states for an approval token.
`ApprovalToken`	interface	An approval token for human-in-the-loop workflow gates. Tokens are bound to…
`TokenValidation`	interface	Result of validating an approval token.
`JoinStrategy`	type	Join strategy for parallel block execution.
`SettleResult`	interface	Result of a parallel block execution with the settle strategy.
`ExecutionScope`	interface	Variable scope for workflow execution.
`DiscretionEvaluator`	interface	Evaluates a discretion condition and returns a boolean judgment.
`ParallelArm`	interface	A single parallel arm to execute.
`ParallelResult`	interface	Result of a parallel block execution.
`WorkflowExecutorConfig`	interface	Configuration options for the workflow executor.
`ResumablePipeline`	interface	Resumable pipeline information returned to callers. T4805 T4798
`PipelineContext`	interface	Pipeline context for session resume. T4805
`StageContext`	interface	Stage context within a pipeline. T4805
`GateResultContext`	interface	Gate result context. T4805 T4804
`EvidenceContext`	interface	Evidence context. T4805 T4804
`TransitionContext`	interface	Transition context. T4805
`TaskContext`	interface	Task context. T4805
`ResumeResult`	interface	Result of a resume operation. T4805
`AutoResumeResult`	interface	Auto-resume detection result. T4805
`FindResumableOptions`	interface	Options for finding resumable pipelines. T4805
`SessionResumeCheckOptions`	interface	Options for session start with resume check. T4805
`SessionResumeCheckResult`	interface	Result of session resume check. T4805
`PrereqCheck`	interface	Prerequisite check result. T4800
`TransitionValidation`	interface	Transition validation result. T4800
`StageState`	interface	Stage state snapshot for state machine. T4800
`StateMachineContext`	interface	State machine context for a pipeline. T4800
`StateTransition`	interface	State transition request. T4800
`StateTransitionResult`	interface	State transition result. T4800
`ContextWindowInput`	interface	Context window input from Claude Code.
`ContextStatus`	type	Context status derived from input.
`HITLLevel`	type	HITL warning level.
`HITLWarning`	interface	HITL warning entry.
`HITLWarningsResult`	interface	HITL warnings result.
`StatuslineStatus`	type	Statusline integration status.
`RoutingEntry`	interface	Routing entry describing the preferred channel for an operation. Derived fro…
`ProviderContext`	interface	Provider capability context for dynamic skill generation.
`IndexMap`	type	Cache index mapping labels/phases to task IDs.
`ImportPackageMeta`	interface	Import package metadata extracted from the export file.
`ImportConflictType`	type	Import conflict types.
`ImportConflictResolution`	type	Import conflict resolution strategies.
`ImportOptions`	interface	Import options for logging context.
`SortableTask`	interface	Minimal task shape needed for topological sorting.
`PipelineStageTaskRow`	interface	Row shape for pipeline + stage + task JOIN.
`PipelineStageRow`	interface	Row shape for pipeline + stage JOIN.
`InsertProjectRegistry`	type
`SelectProjectRegistry`	type
`InsertNexusAuditLog`	type
`SelectNexusAuditLog`	type
`InsertNexusSchemaMeta`	type
`SelectNexusSchemaMeta`	type
`AtomicityResult`	interface
`AtomicityCriterion`	type
`RelatesType`	type	Valid relationship types for relates entries.
`RelatesEntry`	interface	A single relates entry.
`Severity`	type	Impact severity levels.
`DeleteWarning`	interface	An impact warning.
`AffectedTasks`	interface	Affected tasks info.
`DeleteImpact`	interface	Impact analysis.
`DeletePreview`	interface	Full preview result.
`ChildStrategy`	type	Valid child handling strategies.
`StrategyResult`	interface	Result from a strategy handler.
`DiscoveryMethod`	type	Discovery method.
`DiscoveryMatch`	interface	A single discovery match.
`PhaseProgress`	interface	Phase progress information.
`PhaseTransitionValidation`	interface	Validate a phase transition.
`StalenessThresholds`	interface	Staleness thresholds in days.
`StalenessLevel`	type	Staleness classification.
`StalenessInfo`	interface	Staleness assessment for a single task.
`StalenessSummary`	interface	Get staleness summary statistics.

Other Exports

Symbol	Kind	Description
`logger.ts`	file
`platform-paths.ts`	file
`paths.ts`	file
`migration-manager.ts`	file
`sqlite-backup.ts`	file
`status-registry.ts`	file
`AGENT_INSTANCE_STATUSES`	variable	Agent instance status values matching DB CHECK constraint.
`AGENT_TYPES`	variable	Agent type values for classification.
`agentInstances`	variable
`agentErrorLog`	variable
`agent-schema.ts`	file
`WARP_CHAIN_INSTANCE_STATUSES`	variable	Chain instance status values.
`warpChains`	variable	Stored WarpChain definitions (serialized as JSON).
`warpChainInstances`	variable	Runtime chain instances bound to epics.
`chain-schema.ts`	file
`TASK_PRIORITIES`	variable	Task priorities matching DB CHECK constraint on tasks.priority.
`TASK_TYPES`	variable	Task types matching DB CHECK constraint on tasks.type.
`TASK_SIZES`	variable	Task size values matching DB CHECK constraint on tasks.size.
`LIFECYCLE_STAGE_NAMES`	variable	Canonical lifecycle stage names matching DB CHECK constraint on lifecycle_sta…
`LIFECYCLE_GATE_RESULTS`	variable	Gate result values matching DB CHECK constraint on lifecycle_gate_results.res…
`LIFECYCLE_EVIDENCE_TYPES`	variable	Evidence type values matching DB CHECK constraint on lifecycle_evidence.type.
`TOKEN_USAGE_METHODS`	variable	Token measurement methods for central token telemetry.
`TOKEN_USAGE_CONFIDENCE`	variable	Confidence levels for token measurements.
`TOKEN_USAGE_TRANSPORTS`	variable	Transport types for token telemetry.
`TASK_RELATION_TYPES`	variable	Task relation types matching DB CHECK constraint on task_relations.relation_t…
`LIFECYCLE_TRANSITION_TYPES`	variable	Lifecycle transition types matching DB CHECK constraint on lifecycle_transiti…
`EXTERNAL_LINK_TYPES`	variable	External task link types matching DB constraint on external_task_links.link_t…
`SYNC_DIRECTIONS`	variable	Sync direction types matching DB constraint on external_task_links.sync_direc…
`tasks`	variable
`taskDependencies`	variable
`taskRelations`	variable
`sessions`	variable
`taskWorkHistory`	variable
`lifecyclePipelines`	variable
`lifecycleStages`	variable
`lifecycleGateResults`	variable
`lifecycleEvidence`	variable
`lifecycleTransitions`	variable
`manifestEntries`	variable
`pipelineManifest`	variable
`releaseManifests`	variable
`schemaMeta`	variable
`auditLog`	variable	Task change audit log — stores every add/update/complete/delete/archive opera…
`tokenUsage`	variable	Central provider-aware token telemetry for CLI and external adapters. Stores…
`architectureDecisions`	variable	Architecture Decision Records (ADRs) stored in the database. Corresponds to t…
`adrTaskLinks`	variable	ADR-to-Task links (soft FK — tasks can be purged)
`adrRelations`	variable	ADR cross-reference relationships
`externalTaskLinks`	variable	Tracks links between CLEO tasks and external system tasks (Linear, Jira, GitH…
`statusRegistryTable`	variable
`tasks-schema.ts`	file
`BRAIN_DECISION_TYPES`	variable	Decision types from ADR-009.
`BRAIN_CONFIDENCE_LEVELS`	variable	Confidence levels for decisions.
`BRAIN_OUTCOME_TYPES`	variable	Outcome types for decision tracking.
`BRAIN_PATTERN_TYPES`	variable	Pattern types for workflow analysis.
`BRAIN_IMPACT_LEVELS`	variable	Impact levels for patterns.
`BRAIN_LINK_TYPES`	variable	Link types for cross-referencing BRAIN entries with tasks.
`BRAIN_OBSERVATION_TYPES`	variable	Observation types for claude-mem compatible observations.
`BRAIN_OBSERVATION_SOURCE_TYPES`	variable	Source types for observations (how the observation was created).
`BRAIN_MEMORY_TYPES`	variable	Memory entity types for the links table.
`BRAIN_STICKY_STATUSES`	variable	Sticky note status values.
`BRAIN_STICKY_COLORS`	variable	Sticky note colors.
`BRAIN_STICKY_PRIORITIES`	variable	Sticky note priority levels.
`brainDecisions`	variable
`brainPatterns`	variable
`brainLearnings`	variable
`brainObservations`	variable	General-purpose observations — replaces claude-mem’s observations table.
`brainStickyNotes`	variable	Ephemeral sticky notes for quick capture before formal classification.
`brainMemoryLinks`	variable	Cross-references between BRAIN entries and tasks in tasks.db.
`brainSchemaMeta`	variable
`BRAIN_NODE_TYPES`	variable	Node types for PageIndex graph.
`BRAIN_EDGE_TYPES`	variable	Edge types for PageIndex graph.
`brainPageNodes`	variable	Documents/concepts as graph nodes for cross-document linking.
`brainPageEdges`	variable	Directed links between graph nodes.
`brain-schema.ts`	file
`BRAIN_SCHEMA_VERSION`	variable	Schema version for newly created brain databases. Single source of truth.
`brain-sqlite.ts`	file
`projectRegistry`	variable	Central registry of all CLEO projects known to the Nexus.
`nexusAuditLog`	variable	Append-only audit log for all Nexus operations across projects.
`nexusSchemaMeta`	variable	Key-value store for nexus.db schema versioning and metadata.
`nexus-schema.ts`	file
`NEXUS_SCHEMA_VERSION`	variable	Schema version for newly created nexus databases. Single source of truth.
`nexus-sqlite.ts`	file
`SQLITE_SCHEMA_VERSION`	variable	Schema version for newly created databases. Single source of truth.
`sqlite.ts`	file
`parsers.ts`	file
`converters.ts`	file
`SIGNALDOCK_SCHEMA_VERSION`	variable	Schema version for signaldock databases.
`signaldock-sqlite.ts`	file
`cross-db-cleanup.ts`	file
`ERROR_CATALOG`	variable	The unified error catalog. Keyed by numeric ExitCode value.
`error-catalog.ts`	file
`errors.ts`	file
`db-helpers.ts`	file
`registry.ts`	file
`sqlite-data-accessor.ts`	file
`atomic.ts`	file
`backup.ts`	file
`lock.ts`	file
`INTERNAL_HOOK_EVENTS`	variable	CLEO-local coordination events used by the autonomous runtime. These are int…
`CLEO_TO_CAAMP_HOOK_MAP`	variable	Mapping from CLEO internal lifecycle events to CAAMP canonical hook event nam…
`CLEO_INTERNAL_HOOK_MAP`	variable	Internal CLEO lifecycle events that drive autonomous coordination.
`types.ts`	file
`hooks`	variable	Singleton instance of the HookRegistry. Use this instance for all hook opera…
`registry.ts`	file
`json.ts`	file
`git-checkpoint.ts`	file
`data-safety-central.ts`	file
`safety-data-accessor.ts`	file
`data-accessor.ts`	file
`index.ts`	file
`data-safety.ts`	file
`task-store.ts`	file
`mvi-helpers.ts`	file
`show.ts`	file
`pagination.ts`	file
`list.ts`	file
`find.ts`	file
`types.ts`	file
`parse.ts`	file
`link-pipeline.ts`	file
`sync.ts`	file
`evidence.ts`	file
`rcasd-paths.ts`	file
`frontmatter.ts`	file
`PIPELINE_STAGES`	variable
`CONTRIBUTION_STAGE`	variable	Cross-cutting contribution stage. Not part of the pipeline execution order, b…
`STAGE_DEFINITIONS`	variable	Canonical stage definitions with complete metadata. T4800 T4799 - Replaces…
`STAGE_ORDER`	variable	Stage order mapping for quick lookups. T4800
`STAGE_PREREQUISITES`	variable	Prerequisites for each stage - which stages must be completed before entering…
`TRANSITION_RULES`	variable	Allowed transitions between stages. By default, stages progress linearly. Th…
`STAGE_COUNT`	variable	Total number of stages in the pipeline. T4800
`FIRST_STAGE`	variable	First stage in the pipeline. T4800
`LAST_STAGE`	variable	Last stage in the pipeline. T4800
`PLANNING_STAGES`	variable	Planning stages. T4800
`DECISION_STAGES`	variable	Decision stages. T4800
`EXECUTION_STAGES`	variable	Execution stages (canonical). T4800
`VALIDATION_STAGES`	variable	Validation stages. T4800
`DELIVERY_STAGES`	variable	Delivery stages. T4800
`stages.ts`	file
`stage-artifacts.ts`	file
`SKILL_NAME_MAP`	variable	Canonical skill name mapping (user-friendly to ct-prefixed).
`types.ts`	file
`discovery.ts`	file
`token.ts`	file
`dispatch.ts`	file
`STAGE_SKILL_MAP`	variable	Canonical mapping from RCASD-IVTR+C pipeline stages to the primary skill that…
`TIER_0_SKILLS`	variable	Tier 0 skills — always loaded alongside the stage-specific skill. -…
`stage-guidance.ts`	file
`index.ts`	file
`THRESHOLDS`	variable	Context alert thresholds (percentage of context window).
`context-alert.ts`	file
`output.ts`	file
`error-registry.ts`	file
`test-db-helper.ts`	file
`hierarchy.ts`	file
`ENFORCEMENT_PROFILES`	variable
`hierarchy-policy.ts`	file
`STRICTNESS_PRESETS`	variable	All three strictness presets. strict — block on missing AC, require sessio…
`config.ts`	file
`handler-helpers.ts`	file
`types.ts`	file
`decisions.ts`	file
`handoff.ts`	file
`brain-accessor.ts`	file
`typed-query.ts`	file
`brain-row-types.ts`	file
`embedding-local.ts`	file
`EMBEDDING_DIMENSIONS`	variable	Matches the brain_embeddings vec0 table: FLOAT[384].
`brain-embedding.ts`	file
`brain-similarity.ts`	file
`brain-search.ts`	file
`memory-bridge.ts`	file
`memory-bridge-refresh.ts`	file
`brain-retrieval.ts`	file
`audit.ts`	file
`learnings.ts`	file
`session-grade.ts`	file
`adapter-registry.ts`	file
`discovery.ts`	file
`manager.ts`	file
`index.ts`	file
`session-memory-bridge.ts`	file
`decisions.ts`	file
`patterns.ts`	file
`auto-extract.ts`	file
`session-hooks.ts`	file
`task-hooks.ts`	file
`error-hooks.ts`	file
`file-hooks.ts`	file
`notification-hooks.ts`	file
`work-capture-hooks.ts`	file
`agent-hooks.ts`	file
`context-hooks.ts`	file
`index.ts`	file
`assumptions.ts`	file
`brain-links.ts`	file
`session-memory.ts`	file
`deps-ready.ts`	file
`pipeline.ts`	file
`briefing.ts`	file
`find.ts`	file
`session-archive.ts`	file
`session-cleanup.ts`	file
`session-drift.ts`	file
`session-history.ts`	file
`session-show.ts`	file
`session-stats.ts`	file
`session-suspend.ts`	file
`session-switch.ts`	file
`session-view.ts`	file
`provider-detection.ts`	file
`index.ts`	file
`session-enforcement.ts`	file
`enforcement.ts`	file
`TASK_PIPELINE_STAGES`	variable	Ordered pipeline stages (RCASD-IVTR+C). This matches lifecycle/stages.ts PIPE…
`pipeline-stage.ts`	file
`EPIC_MIN_AC`	variable	Minimum acceptance criteria count required for epic creation in strict mode.
`TASK_MIN_AC`	variable	Minimum acceptance criteria count for regular tasks.
`epic-enforcement.ts`	file
`VALID_PRIORITIES`	variable	Valid string priority values.
`add.ts`	file
`index.ts`	file
`audit-prune.ts`	file
`hash.ts`	file
`json-schema-validator.ts`	file
`schema-management.ts`	file
`schema-integrity.ts`	file
`project-detect.ts`	file
`injection.ts`	file
`REQUIRED_CLEO_SUBDIRS`	variable	Required subdirectories under .cleo/.
`CLEO_GITIGNORE_FALLBACK`	variable	Embedded fallback for .cleo/.gitignore content (deny-by-default).
`REQUIRED_GLOBAL_SUBDIRS`	variable	Required subdirectories under the global ~/.cleo/ home. These are infrastruct…
`STALE_GLOBAL_ENTRIES`	variable	Stale entries that must NOT exist at the global ~/.cleo/ level. These were pr…
`scaffold.ts`	file
`discovery.ts`	file
`MANAGED_HOOKS`	variable	Git hooks managed by CLEO.
`hooks.ts`	file
`agent-outputs.ts`	file
`migrate-json-to-sqlite.ts`	file
`registry.ts`	file
`stack.ts`	file
`architecture.ts`	file
`structure.ts`	file
`conventions.ts`	file
`testing.ts`	file
`integrations.ts`	file
`concerns.ts`	file
`store.ts`	file
`index.ts`	file
`init.ts`	file
`bootstrap.ts`	file
`caamp-init.ts`	file
`export.ts`	file
`import.ts`	file
`execution-learning.ts`	file
`MAX_TASKS_PER_AGENT`	variable	Maximum number of tasks that can be concurrently assigned to one agent. Used…
`agent-registry.ts`	file
`capacity.ts`	file
`HEARTBEAT_INTERVAL_MS`	variable	Default heartbeat interval (30 seconds) per BRAIN spec.
`STALE_THRESHOLD_MS`	variable	Default staleness threshold: 3 minutes without a heartbeat.
`health-monitor.ts`	file
`DEFAULT_RETRY_POLICY`	variable	Default retry policy matching the BRAIN specification.
`retry.ts`	file
`index.ts`	file
`types.ts`	file
`prediction.ts`	file
`adaptive-validation.ts`	file
`dependency-check.ts`	file
`graph-ops.ts`	file
`impact.ts`	file
`patterns.ts`	file
`index.ts`	file
`query.ts`	file
`discover.ts`	file
`permissions.ts`	file
`index.ts`	file
`getTaskHistory`	variable	Get task work history (canonical verb alias for dispatch layer). T5323
`index.ts`	file
`complete.ts`	file
`validation-rules.ts`	file
`update.ts`	file
`workspace.ts`	file
`deps.ts`	file
`analyze.ts`	file
`context.ts`	file
`hierarchy.ts`	file
`waves.ts`	file
`status.ts`	file
`index.ts`	file
`link-store.ts`	file
`reconciliation-engine.ts`	file
`index.ts`	file
`artifacts.ts`	file
`changelog-writer.ts`	file
`release-config.ts`	file
`channel.ts`	file
`SUPPORTED_PLATFORMS`	variable	All supported platforms.
`ci.ts`	file
`github-pr.ts`	file
`guards.ts`	file
`version-bump.ts`	file
`release-manifest.ts`	file
`index.ts`	file
`SNAPSHOT_VERSION`	variable	Version of the snapshot schema. Increment on breaking changes.
`snapshot.ts`	file
`types.ts`	file
`archive.ts`	file
`convert.ts`	file
`id.ts`	file
`create.ts`	file
`list.ts`	file
`purge.ts`	file
`show.ts`	file
`index.ts`	file
`archive.ts`	file
`delete.ts`	file
`cleo.ts`	file
`CORE_PROTECTED_FILES`	variable	Configuration files relative to .cleo/ that MUST remain tracked by project gi…
`constants.ts`	file
`engine-result.ts`	file
`export.ts`	file
`export-tasks.ts`	file
`help.ts`	file
`transfer-types.ts`	file
`import-remap.ts`	file
`import-tasks.ts`	file
`index.ts`	file
`find.ts`	file
`list.ts`	file
`show.ts`	file
`validate.ts`	file
`index.ts`	file
`adapter.ts`	file
`capability-check.ts`	file
`index.ts`	file
`SUPPORTED_EXTENSIONS`	variable	All supported file extensions.
`SUPPORTED_LANGUAGES`	variable	All supported languages.
`tree-sitter-languages.ts`	file
`parser.ts`	file
`outline.ts`	file
`search.ts`	file
`unfold.ts`	file
`index.ts`	file
`store.ts`	file
`index.ts`	file
`conduit-client.ts`	file
`http-transport.ts`	file
`local-transport.ts`	file
`sse-transport.ts`	file
`factory.ts`	file
`index.ts`	file
`index.ts`	file
`HookPayloadSchema`	variable	Zod schema for `HookPayload`.
`SessionStartPayloadSchema`	variable	Zod schema for `SessionStartPayload`.
`OnSessionStartPayloadSchema`	variable
`SessionEndPayloadSchema`	variable	Zod schema for `SessionEndPayload`.
`OnSessionEndPayloadSchema`	variable
`PreToolUsePayloadSchema`	variable	Zod schema for `PreToolUsePayload`.
`OnToolStartPayloadSchema`	variable
`PostToolUsePayloadSchema`	variable	Zod schema for `PostToolUsePayload`.
`OnToolCompletePayloadSchema`	variable
`NotificationPayloadSchema`	variable	Zod schema for `NotificationPayload`.
`OnFileChangePayloadSchema`	variable
`PostToolUseFailurePayloadSchema`	variable	Zod schema for `PostToolUseFailurePayload`.
`OnErrorPayloadSchema`	variable
`PromptSubmitPayloadSchema`	variable	Zod schema for `PromptSubmitPayload`.
`OnPromptSubmitPayloadSchema`	variable
`ResponseCompletePayloadSchema`	variable	Zod schema for `ResponseCompletePayload`.
`OnResponseCompletePayloadSchema`	variable
`SubagentStartPayloadSchema`	variable	Zod schema for `SubagentStartPayload`.
`SubagentStopPayloadSchema`	variable	Zod schema for `SubagentStopPayload`.
`PreCompactPayloadSchema`	variable	Zod schema for `PreCompactPayload`.
`PostCompactPayloadSchema`	variable	Zod schema for `PostCompactPayload`.
`ConfigChangePayloadSchema`	variable	Zod schema for `ConfigChangePayload`.
`OnWorkAvailablePayloadSchema`	variable	Zod schema for `OnWorkAvailablePayload`.
`OnAgentSpawnPayloadSchema`	variable	Zod schema for `OnAgentSpawnPayload`.
`OnAgentCompletePayloadSchema`	variable	Zod schema for `OnAgentCompletePayload`.
`OnCascadeStartPayloadSchema`	variable	Zod schema for `OnCascadeStartPayload`.
`OnPatrolPayloadSchema`	variable	Zod schema for `OnPatrolPayload`.
`payload-schemas.ts`	file
`index.ts`	file
`index.ts`	file
`BUILD_CONFIG`	variable	BUILD CONFIGURATION - AUTO-GENERATED FILE This file is generated by dev/gene…
`build-config.ts`	file
`diagnostics.ts`	file
`template-parser.ts`	file
`create.ts`	file
`index.ts`	file
`retry.ts`	file
`index.ts`	file
`brain-lifecycle.ts`	file
`brain-migration.ts`	file
`index.ts`	file	Research commands and manifest operations. T4465 T4454
`common.ts`	file
`otel-integration.ts`	file
`ab-test.ts`	file
`aggregation.ts`	file
`enums.ts`	file
`token-estimation.ts`	file
`index.ts`	file
`checksum.ts`	file
`logger.ts`	file
`storage-preflight.ts`	file
`preflight.ts`	file
`state.ts`	file
`validate.ts`	file
`index.ts`	file
`deps.ts`	file
`transfer.ts`	file
`index.ts`	file
`PINO_LEVEL_VALUES`	variable	Numeric pino level values for comparison.
`types.ts`	file
`log-filter.ts`	file
`log-parser.ts`	file
`log-reader.ts`	file
`index.ts`	file
`index.ts`	file
`phase.ts`	file
`index.ts`	file
`index.ts`	file
`index.ts`	file
`index.ts`	file
`capability-matrix.ts`	file
`index.ts`	file
`id-generator.ts`	file
`VALID_DOMAINS`	variable	Known enum values for CLEO domains
`VALID_GATEWAYS`	variable
`VALID_MANIFEST_STATUSES`	variable
`VALID_LIFECYCLE_STAGE_STATUSES`	variable
`ALL_VALID_STATUSES`	variable
`VALID_PRIORITIES`	variable
`DEFAULT_RATE_LIMITS`	variable	Default rate limit configurations per operation type
`input-sanitization.ts`	file
`index.ts`	file
`config.ts`	file
`install.ts`	file
`registry.ts`	file
`subagent.ts`	file
`install.ts`	file
`contribution.ts`	file
`research.ts`	file
`resolver.ts`	file
`marketplace.ts`	file
`spawn.ts`	file
`startup.ts`	file
`validator.ts`	file
`skill-paths.ts`	file
`test-utility.ts`	file
`validation.ts`	file
`version.ts`	file
`index.ts`	file
`index.ts`	file
`spawnRegistry`	variable	Singleton registry instance. Use this instance for all spawn adapter registr…
`adapter-registry.ts`	file
`index.ts`	file
`workflow-telemetry.ts`	file
`index.ts`	file
`archive-analytics.ts`	file
`archive-stats.ts`	file
`audit.ts`	file
`backup.ts`	file
`cleanup.ts`	file
`file-utils.ts`	file
`PLATFORM`	variable	Cached platform value.
`MINIMUM_NODE_MAJOR`	variable	Minimum required Node.js major version.
`platform.ts`	file
`checks.ts`	file
`health.ts`	file
`inject-generate.ts`	file
`labels.ts`	file
`metrics.ts`	file
`migrate.ts`	file
`runtime.ts`	file
`safestop.ts`	file
`index.ts`	file
`index.ts`	file
`parser.ts`	file
`index.ts`	file
`ALIASES_VERSION`	variable	Current alias version.
`aliases.ts`	file
`changelog.ts`	file
`command-registry.ts`	file
`flags.ts`	file
`index.ts`	file
`taskStatusSchema`	variable	Zod enum schema for task statuses.
`taskPrioritySchema`	variable	Zod enum schema for task priorities.
`taskTypeSchema`	variable	Zod enum schema for task types.
`taskSizeSchema`	variable	Zod enum schema for task sizes.
`sessionStatusSchema`	variable	Zod enum schema for session statuses.
`lifecyclePipelineStatusSchema`	variable	Zod enum schema for lifecycle pipeline statuses.
`lifecycleStageStatusSchema`	variable	Zod enum schema for lifecycle stage statuses.
`lifecycleStageNameSchema`	variable	Zod enum schema for lifecycle stage names.
`lifecycleGateResultSchema`	variable	Zod enum schema for lifecycle gate results.
`lifecycleEvidenceTypeSchema`	variable	Zod enum schema for lifecycle evidence types.
`adrStatusSchema`	variable	Zod enum schema for ADR statuses.
`gateStatusSchema`	variable	Zod enum schema for gate statuses.
`manifestStatusSchema`	variable	Zod enum schema for manifest statuses.
`tokenUsageMethodSchema`	variable	Zod enum schema for token usage measurement methods.
`tokenUsageConfidenceSchema`	variable	Zod enum schema for token usage confidence levels.
`tokenUsageTransportSchema`	variable	Zod enum schema for token usage transports.
`taskRelationTypeSchema`	variable	Zod enum schema for task relation types.
`externalLinkTypeSchema`	variable	Zod enum schema for external task link types.
`syncDirectionSchema`	variable	Zod enum schema for sync directions.
`lifecycleTransitionTypeSchema`	variable	Zod enum schema for lifecycle transition types.
`brainObservationTypeSchema`	variable	Zod enum schema for brain observation types.
`brainObservationSourceTypeSchema`	variable	Zod enum schema for brain observation source types.
`brainDecisionTypeSchema`	variable	Zod enum schema for brain decision types.
`brainConfidenceLevelSchema`	variable	Zod enum schema for brain confidence levels.
`brainOutcomeTypeSchema`	variable	Zod enum schema for brain outcome types.
`brainPatternTypeSchema`	variable	Zod enum schema for brain pattern types.
`brainImpactLevelSchema`	variable	Zod enum schema for brain impact levels.
`brainLinkTypeSchema`	variable	Zod enum schema for brain link types.
`brainMemoryTypeSchema`	variable	Zod enum schema for brain memory entity types.
`brainStickyStatusSchema`	variable	Zod enum schema for brain sticky note statuses.
`brainStickyColorSchema`	variable	Zod enum schema for brain sticky note colors.
`brainStickyPrioritySchema`	variable	Zod enum schema for brain sticky note priorities.
`brainNodeTypeSchema`	variable	Zod enum schema for brain page node types.
`brainEdgeTypeSchema`	variable	Zod enum schema for brain page edge types.
`insertTaskSchema`	variable
`selectTaskSchema`	variable
`insertTaskDependencySchema`	variable
`selectTaskDependencySchema`	variable
`insertTaskRelationSchema`	variable
`selectTaskRelationSchema`	variable
`insertSessionSchema`	variable
`selectSessionSchema`	variable
`insertWorkHistorySchema`	variable
`selectWorkHistorySchema`	variable
`insertLifecyclePipelineSchema`	variable
`selectLifecyclePipelineSchema`	variable
`insertLifecycleStageSchema`	variable
`selectLifecycleStageSchema`	variable
`insertLifecycleGateResultSchema`	variable
`selectLifecycleGateResultSchema`	variable
`insertLifecycleEvidenceSchema`	variable
`selectLifecycleEvidenceSchema`	variable
`insertLifecycleTransitionSchema`	variable
`selectLifecycleTransitionSchema`	variable
`insertSchemaMetaSchema`	variable
`selectSchemaMetaSchema`	variable
`insertAuditLogSchema`	variable	Zod schema for validating audit log insert payloads. T4848
`AuditLogInsertSchema`	variable	Canonical named export for audit log insert schema (T4848). Alias for insertA…
`selectAuditLogSchema`	variable
`AuditLogSelectSchema`	variable	Canonical named export for audit log select schema (T4848). Alias for selectA…
`insertArchitectureDecisionSchema`	variable
`selectArchitectureDecisionSchema`	variable
`insertTokenUsageSchema`	variable
`selectTokenUsageSchema`	variable
`insertManifestEntrySchema`	variable
`selectManifestEntrySchema`	variable
`insertPipelineManifestSchema`	variable
`selectPipelineManifestSchema`	variable
`insertReleaseManifestSchema`	variable
`selectReleaseManifestSchema`	variable
`insertExternalTaskLinkSchema`	variable
`selectExternalTaskLinkSchema`	variable
`insertAgentInstanceSchema`	variable
`selectAgentInstanceSchema`	variable
`insertAgentErrorLogSchema`	variable
`selectAgentErrorLogSchema`	variable
`agentInstanceStatusSchema`	variable	Zod enum schema for agent instance statuses.
`agentTypeSchema`	variable	Zod enum schema for agent types.
`validation-schemas.ts`	file
`compliance.ts`	file
`docs-sync.ts`	file
`CACHE_VERSION`	variable
`CACHE_TTL_SECONDS`	variable
`project-cache.ts`	file
`utils.ts`	file
`index.ts`	file
`VALID_OPERATIONS`	variable
`FIELD_LIMITS`	variable	Field length limits matching the Bash implementation.
`VAL_SUCCESS`	variable	Validation result exit codes.
`VAL_SCHEMA_ERROR`	variable
`VAL_SEMANTIC_ERROR`	variable
`VAL_BOTH_ERRORS`	variable
`engine.ts`	file
`gap-check.ts`	file
`manifest.ts`	file
`protocol-common.ts`	file
`VERIFICATION_GATE_ORDER`	variable
`VERIFICATION_VALID_AGENTS`	variable
`verification.ts`	file
`index.ts`	file
`project-info.ts`	file
`index.ts`	file
`index.ts`	file	Backfill module: retroactively add AC and verification metadata to existing t…
`PROTOCOL_RULES`	variable	Protocol rule registry
`protocol-rules.ts`	file
`protocol-types.ts`	file
`protocolEnforcer`	variable	Default protocol enforcer instance
`protocol-enforcement.ts`	file
`provider-hooks.ts`	file
`chain-validation.ts`	file
`chain-store.ts`	file
`PROTOCOL_TYPES`	variable	All supported protocol types. The canonical set covers all 9 RCASD-IVTR pipe…
`PROTOCOL_EXIT_CODES`	variable	Map protocol types to exit codes. Pipeline protocols use the 60-67 orchestra…
`protocol-validators.ts`	file
`DEFAULT_CHAIN_ID`	variable
`DEFAULT_PROTOCOL_STAGE_MAP`	variable	Stage mapping for protocol validation gates in the default chain. Cross-cutt…
`default-chain.ts`	file
`tessera-engine.ts`	file
`brain-maintenance.ts`	file
`claude-mem-migration.ts`	file
`brain-reasoning.ts`	file
`engine-compat.ts`	file
`pipeline-manifest-sqlite.ts`	file
`model-provider-registry.ts`	file
`token-service.ts`	file
`parallel.ts`	file
`skill-ops.ts`	file
`unblock.ts`	file
`validate-spawn.ts`	file
`context-inject.ts`	file
`session-id.ts`	file
`session-store.ts`	file
`relates.ts`	file
`cancel-ops.ts`	file
`task-ops.ts`	file
`analyze.ts`	file
`labels.ts`	file
`provider.ts`	file
`index.ts`	file
`migration-sqlite.ts`	file
`repair.ts`	file
`upgrade.ts`	file
`GATE_SEQUENCE`	variable	Export gate layer sequence for external use
`WORKFLOW_GATE_DEFINITIONS`	variable	Complete workflow gate definitions per Section 7.2
`WORKFLOW_GATE_SEQUENCE`	variable	Ordered workflow gate sequence per Section 7.1
`operation-verification-gates.ts`	file
`GATE_VALIDATION_RULES`	variable	Validation rule definitions for reuse
`VALID_WORKFLOW_AGENTS`	variable	Valid workflow gate agent names per Section 7.2
`VALID_WORKFLOW_GATE_STATUSES`	variable	Valid workflow gate status values per Section 7.3
`operation-gate-validators.ts`	file
`param-utils.ts`	file
`_shared.ts`	file
`architecture-decision.ts`	file
`artifact-publish.ts`	file
`consensus.ts`	file
`contribution.ts`	file
`decomposition.ts`	file
`implementation.ts`	file
`provenance.ts`	file
`release.ts`	file
`research.ts`	file
`specification.ts`	file
`testing.ts`	file
`validation.ts`	file
`schema-validator.ts`	file
`validate-ops.ts`	file
`bootstrap.ts`	file
`critical-path.ts`	file
`precedence-types.ts`	file
`precedence-integration.ts`	file
`plan.ts`	file
`credentials.ts`	file
`agent-registry-accessor.ts`	file
`internal.ts`	file
`audit-prune.test.ts`	file
`caamp-skill-install.test.ts`	file
`cli-parity.test.ts`	file
`config.test.ts`	file
`error-catalog.test.ts`	file
`hooks.test.ts`	file
`human-output.test.ts`	file
`index-api-compat.test.ts`	file
`init-e2e.test.ts`	file
`injection-chain.test.ts`	file
`injection-mvi-tiers.test.ts`	file
`injection-shared.test.ts`	file
`logger.test.ts`	file
`paths.test.ts`	file
`project-info.test.ts`	file
`rcasd-index.ts`	file
`rcsd-pipeline-e2e.test.ts`	file
`remote.test.ts`	file
`scaffold.test.ts`	file
`schema-management.test.ts`	file
`schema.test.ts`	file
`sharing.test.ts`	file
`snapshot.test.ts`	file
`upgrade.test.ts`	file
`discovery.test.ts`	file
`manager.test.ts`	file
`agent-registry.test.ts`	file
`capacity.test.ts`	file
`execution-learning.test.ts`	file
`health-monitor.test.ts`	file
`registry.test.ts`	file
`retry.test.ts`	file
`types.ts`	file
`approval.ts`	file
`context-builder.ts`	file
`discretion.ts`	file
`parallel-runner.ts`	file
`workflow-executor.ts`	file
`index.ts`	file
`cant-agent-parse.test.ts`	file
`summary.ts`	file
`sync.test.ts`	file
`dual-api-e2e.test.ts`	file
`local-credential-flow.test.ts`	file
`local-transport.test.ts`	file
`sse-transport.test.ts`	file
`provider-hooks.test.ts`	file
`registry.test.ts`	file
`error-hooks.test.ts`	file
`file-hooks.test.ts`	file
`hook-automation-e2e.test.ts`	file
`session-hooks.test.ts`	file
`task-hooks.test.ts`	file
`adaptive-validation.test.ts`	file
`impact.test.ts`	file
`patterns.test.ts`	file
`prediction.test.ts`	file
`retry.test.ts`	file
`chain-composition.ts`	file
`consolidate-rcasd.ts`	file
`resume.ts`	file
`state-machine.ts`	file
`chain-store.test.ts`	file
`consolidate-rcasd.test.ts`	file
`default-chain.test.ts`	file
`frontmatter.test.ts`	file
`lifecycle.test.ts`	file
`pipeline.integration.test.ts`	file
`rcasd-paths.test.ts`	file
`resume-schema-contract.test.ts`	file
`stage-record-provenance.integration.test.ts`	file
`tessera-engine.test.ts`	file
`embedding-queue.ts`	file
`embedding-worker.ts`	file
`auto-extract.test.ts`	file
`brain-automation.test.ts`	file
`brain-embedding.test.ts`	file
`brain-links.test.ts`	file
`brain-migration.test.ts`	file
`brain-retrieval.test.ts`	file
`brain-search.test.ts`	file
`claude-mem-migration.test.ts`	file
`decisions.test.ts`	file
`engine-compat.test.ts`	file
`memory-bridge.test.ts`	file
`pipeline-manifest-sqlite.test.ts`	file
`session-memory.test.ts`	file
`model-provider-registry.test.ts`	file
`provider-detection.test.ts`	file
`checksum.test.ts`	file
`logger.test.ts`	file
`migration-failure.integration.test.ts`	file
`migration.test.ts`	file
`state.test.ts`	file
`validate.test.ts`	file
`deps.test.ts`	file
`nexus-e2e.test.ts`	file
`permissions.test.ts`	file
`query.test.ts`	file
`reconcile.test.ts`	file
`registry.test.ts`	file
`transfer.test.ts`	file
`index.test.ts`	file
`log-filter.test.ts`	file
`log-parser.test.ts`	file
`log-reader.test.ts`	file
`autonomous-spec.test.ts`	file
`orchestration.test.ts`	file
`protocol-validators.test.ts`	file
`deps.test.ts`	file
`phases.test.ts`	file
`artifacts.test.ts`	file
`cancel-release.test.ts`	file
`changelog-writer.test.ts`	file
`push-policy.test.ts`	file
`release.test.ts`	file
`allocate.test.ts`	file
`context-monitor.ts`	file
`hitl-warnings.ts`	file
`statusline-setup.ts`	file
`briefing-blocked.test.ts`	file
`briefing.test.ts`	file
`handoff-integration.test.ts`	file
`handoff.test.ts`	file
`index.test.ts`	file
`session-cleanup.test.ts`	file
`session-edge-cases.test.ts`	file
`session-find.test.ts`	file
`session-grade.integration.test.ts`	file
`session-grade.test.ts`	file
`session-memory-bridge.test.ts`	file
`sessions.test.ts`	file
`routing-table.ts`	file
`dynamic-skill-generator.ts`	file
`discovery.test.ts`	file
`dispatch.test.ts`	file
`dynamic-skill-generator.test.ts`	file
`manifests.test.ts`	file
`precedence.test.ts`	file
`routing-table.test.ts`	file
`skill-paths.test.ts`	file
`test-utility.test.ts`	file
`token.test.ts`	file
`validation.test.ts`	file
`version.test.ts`	file
`subagent.test.ts`	file
`spawn-tier.test.ts`	file
`adapter-registry.test.ts`	file
`stats.test.ts`	file
`purge.test.ts`	file
`cache.ts`	file
`import-logging.ts`	file
`import-sort.ts`	file
`lifecycle-store.ts`	file
`insertProjectRegistrySchema`	variable
`selectProjectRegistrySchema`	variable
`insertNexusAuditLogSchema`	variable
`selectNexusAuditLogSchema`	variable
`insertNexusSchemaMetaSchema`	variable
`selectNexusSchemaMetaSchema`	variable
`nexus-validation-schemas.ts`	file
`schema.ts`	file
`atomic.test.ts`	file
`backup.test.ts`	file
`brain-accessor-pageindex.test.ts`	file
`brain-accessor.test.ts`	file
`brain-pageindex.test.ts`	file
`brain-schema.test.ts`	file
`brain-vec.test.ts`	file
`collision-detection.test.ts`	file
`data-safety-central.test.ts`	file
`db-helpers.test.ts`	file
`e2e-safety-integration.test.ts`	file
`git-checkpoint.test.ts`	file
`idempotent-migration.test.ts`	file
`import-logging.test.ts`	file
`import-sort.test.ts`	file
`json.test.ts`	file
`lifecycle-schema-parity.test.ts`	file
`migration-integration.test.ts`	file
`migration-retry.test.ts`	file
`migration-safety.test.ts`	file
`migration-sqlite.test.ts`	file
`performance-safety.test.ts`	file
`project-detect.test.ts`	file
`project-registry.test.ts`	file
`provider.test.ts`	file
`relations.test.ts`	file
`safety-accessor.test.ts`	file
`sequence-validation.test.ts`	file
`session-store.test.ts`	file
`sqlite-backup.test.ts`	file
`sqlite.test.ts`	file
`task-store.test.ts`	file
`write-verification.test.ts`	file
`cleanup.test.ts`	file
`health.test.ts`	file
`start-deps.test.ts`	file
`ATOMICITY_CRITERIA`	variable
`atomicity.ts`	file
`crossref-extract.ts`	file
`delete-preview.ts`	file
`VALID_STRATEGIES`	variable
`deletion-strategy.ts`	file
`graph-cache.ts`	file
`graph-rag.ts`	file
`phase-tracking.ts`	file
`size-weighting.ts`	file
`DEFAULT_THRESHOLDS`	variable	Default thresholds.
`staleness.ts`	file
`add.test.ts`	file
`archive.test.ts`	file
`assignee.test.ts`	file
`atomicity.test.ts`	file
`cancel-ops.test.ts`	file
`complete-unblocks.test.ts`	file
`complete.test.ts`	file
`delete.test.ts`	file
`dependency-check.test.ts`	file
`deps-ready.test.ts`	file
`epic-enforcement.test.ts`	file
`find.test.ts`	file
`graph-ops.test.ts`	file
`hierarchy-policy.test.ts`	file
`hierarchy.test.ts`	file
`id-generator.test.ts`	file
`labels.test.ts`	file
`list.test.ts`	file
`minimal-test.test.ts`	file
`phase-tracking.test.ts`	file
`pipeline-stage.test.ts`	file
`plan-priority.test.ts`	file
`priority-normalization.test.ts`	file
`relates.test.ts`	file
`show-deps.test.ts`	file
`show.test.ts`	file
`staleness.test.ts`	file
`task-ops-depends.test.ts`	file
`update.test.ts`	file
`chain-validation.test.ts`	file
`compliance.test.ts`	file
`docs-sync.test.ts`	file
`doctor-gitignore.test.ts`	file
`doctor-injection.test.ts`	file
`doctor.test.ts`	file
`engine.test.ts`	file
`manifest.test.ts`	file
`protocol-common.test.ts`	file
`verification.test.ts`	file

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@forge-ts/.

@forge-ts/adapters

@forge-ts/caamp

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@forge-ts/core

@forge-ts/cleo

@forge-ts/contracts

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@forge-ts/runtime

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Functions & Classes

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