@cleocode/core 2026.4.0 → 2026.4.2

package/dist/memory/index.d.ts

@@ -1,76 +1,177 @@
 /**
  * Research commands and manifest operations.
+ *
+ * @packageDocumentation
  * @task T4465
  * @epic T4454
  */
 import type { DataAccessor } from '../store/data-accessor.js';
 /** Research entry attached to a task. */
 export interface ResearchEntry {
+    /** Unique research entry identifier. */
     id: string;
+    /** Task ID this research is linked to. */
     taskId: string;
+    /** Research topic or question. */
     topic: string;
+    /** Accumulated research findings. */
     findings: string[];
+    /** Source URLs or references. */
     sources: string[];
+    /** Current research status. */
     status: 'pending' | 'complete' | 'partial';
+    /** ISO timestamp of creation. */
     createdAt: string;
+    /** ISO timestamp of last update. */
     updatedAt: string;
 }
 /** Manifest entry (JSONL line). */
 export interface ManifestEntry {
+    /** Unique manifest entry identifier. */
     id: string;
+    /** Output file path for this entry. */
     file: string;
+    /** Human-readable title of the research output. */
     title: string;
+    /** ISO date string when the entry was created. */
     date: string;
+    /** Completion status of the research. */
     status: 'completed' | 'partial' | 'blocked';
+    /** Type of agent that produced this entry. */
     agent_type: string;
+    /** Topic tags associated with the entry. */
     topics: string[];
+    /** Key findings from the research. */
     key_findings: string[];
+    /** Whether the findings are actionable. */
     actionable: boolean;
+    /** Items that need follow-up investigation. */
     needs_followup: string[];
+    /** Task IDs linked to this manifest entry. */
     linked_tasks: string[];
 }
 /** Options for adding research. */
 export interface AddResearchOptions {
+    /** Task ID to attach the research to. */
     taskId: string;
+    /** Research topic or question. */
     topic: string;
+    /** Initial findings (if any). */
     findings?: string[];
+    /** Source URLs or references. */
     sources?: string[];
 }
 /** Options for listing research. */
 export interface ListResearchOptions {
+    /** Filter by linked task ID. */
     taskId?: string;
+    /** Filter by research status. */
     status?: 'pending' | 'complete' | 'partial';
 }
 /** Manifest query options. */
 export interface ManifestQueryOptions {
+    /** Filter by completion status. */
     status?: string;
+    /** Filter by agent type. */
     agentType?: string;
+    /** Filter by topic tag. */
     topic?: string;
+    /** Filter by linked task ID. */
     taskId?: string;
+    /** Maximum entries to return. */
     limit?: number;
 }
 /**
  * Add a research entry.
+ *
+ * @param options - Research entry data including taskId and topic
+ * @param cwd - Optional working directory for path resolution
+ * @param accessor - Data accessor for task validation
+ * @returns The created ResearchEntry
+ *
+ * @remarks
+ * Validates the linked task exists, generates a unique ID, and persists
+ * the entry to research.json. Logs the operation to the audit log.
+ *
+ * @example
+ * ```typescript
+ * const entry = await addResearch({ taskId: 'T042', topic: 'Auth patterns' }, '/project', accessor);
+ * ```
+ *
  * @task T4465
  */
 export declare function addResearch(options: AddResearchOptions, cwd?: string, accessor?: DataAccessor): Promise<ResearchEntry>;
 /**
  * Show a specific research entry.
+ *
+ * @param researchId - The research entry ID to look up
+ * @param cwd - Optional working directory for path resolution
+ * @returns The matching ResearchEntry
+ *
+ * @remarks
+ * Throws a CleoError with NOT_FOUND if the entry does not exist.
+ *
+ * @example
+ * ```typescript
+ * const entry = await showResearch('Rlk1abc2', '/project');
+ * ```
+ *
  * @task T4465
  */
 export declare function showResearch(researchId: string, cwd?: string): Promise<ResearchEntry>;
 /**
  * List research entries with optional filtering.
+ *
+ * @param options - Optional filters for taskId and status
+ * @param cwd - Optional working directory for path resolution
+ * @returns Filtered array of ResearchEntry records
+ *
+ * @remarks
+ * Returns all entries when no filters are provided.
+ *
+ * @example
+ * ```typescript
+ * const entries = await listResearch({ status: 'pending' }, '/project');
+ * ```
+ *
  * @task T4465
  */
 export declare function listResearch(options?: ListResearchOptions, cwd?: string): Promise<ResearchEntry[]>;
 /**
  * List pending research entries.
+ *
+ * @param cwd - Optional working directory for path resolution
+ * @returns Array of research entries with status "pending"
+ *
+ * @remarks
+ * Convenience wrapper around listResearch with status filter pre-set.
+ *
+ * @example
+ * ```typescript
+ * const pending = await pendingResearch('/project');
+ * ```
+ *
  * @task T4465
  */
 export declare function pendingResearch(cwd?: string): Promise<ResearchEntry[]>;
 /**
  * Link a research entry to a task.
+ *
+ * @param researchId - The research entry ID to link
+ * @param taskId - The target task ID
+ * @param cwd - Optional working directory for path resolution
+ * @param accessor - Data accessor for task validation
+ * @returns Confirmation with researchId and taskId
+ *
+ * @remarks
+ * Updates the research entry's taskId field and persists the change.
+ * Validates both the research entry and target task exist.
+ *
+ * @example
+ * ```typescript
+ * await linkResearch('Rlk1abc2', 'T050', '/project', accessor);
+ * ```
+ *
  * @task T4465
  */
 export declare function linkResearch(researchId: string, taskId: string, cwd?: string, accessor?: DataAccessor): Promise<{
@@ -79,6 +180,21 @@ export declare function linkResearch(researchId: string, taskId: string, cwd?: s
 }>;
 /**
  * Update research findings.
+ *
+ * @param researchId - The research entry ID to update
+ * @param updates - Fields to update (findings, sources, and/or status)
+ * @param cwd - Optional working directory for path resolution
+ * @returns The updated ResearchEntry
+ *
+ * @remarks
+ * Only provided fields are updated; others are left unchanged.
+ * Updates the `updatedAt` timestamp automatically.
+ *
+ * @example
+ * ```typescript
+ * const entry = await updateResearch('Rlk1abc2', { status: 'complete', findings: ['JWT is used'] });
+ * ```
+ *
  * @task T4465
  */
 export declare function updateResearch(researchId: string, updates: {
@@ -88,6 +204,19 @@ export declare function updateResearch(researchId: string, updates: {
 }, cwd?: string): Promise<ResearchEntry>;
 /**
  * Get research statistics.
+ *
+ * @param cwd - Optional working directory for path resolution
+ * @returns Total count and breakdowns by status and topic
+ *
+ * @remarks
+ * Aggregates all research entries into status and topic distributions.
+ *
+ * @example
+ * ```typescript
+ * const stats = await statsResearch('/project');
+ * console.log(`${stats.total} entries, ${stats.byStatus.pending ?? 0} pending`);
+ * ```
+ *
  * @task T4474
  */
 export declare function statsResearch(cwd?: string): Promise<{
@@ -97,13 +226,39 @@ export declare function statsResearch(cwd?: string): Promise<{
 }>;
 /**
  * Get research entries linked to a specific task.
+ *
+ * @param taskId - The task ID to find linked research for
+ * @param cwd - Optional working directory for path resolution
+ * @returns Array of research entries linked to the given task
+ *
+ * @remarks
+ * Filters research entries by taskId. Throws if taskId is empty.
+ *
+ * @example
+ * ```typescript
+ * const linked = await linksResearch('T042', '/project');
+ * ```
+ *
  * @task T4474
  */
 export declare function linksResearch(taskId: string, cwd?: string): Promise<ResearchEntry[]>;
 /**
  * Archive old research entries by status.
- * Moves 'complete' entries older than a threshold to an archive,
- * or returns summary of archivable entries.
+ * Moves 'complete' entries to an archive and keeps non-complete ones.
+ *
+ * @param cwd - Optional working directory for path resolution
+ * @returns Summary with count of archived and remaining entries
+ *
+ * @remarks
+ * Removes all "complete" entries from the active research file and reports
+ * how many were archived vs. retained.
+ *
+ * @example
+ * ```typescript
+ * const result = await archiveResearch('/project');
+ * console.log(`Archived ${result.entriesArchived} entries`);
+ * ```
+ *
  * @task T4474
  */
 export declare function archiveResearch(cwd?: string): Promise<{
@@ -113,49 +268,142 @@ export declare function archiveResearch(cwd?: string): Promise<{
 }>;
 /**
  * Read manifest entries from MANIFEST.jsonl.
+ *
+ * @param cwd - Optional working directory for path resolution
+ * @returns Array of parsed ManifestEntry records from the JSONL file
+ *
+ * @remarks
+ * Reads the file line by line, skipping blank and malformed lines.
+ * Returns an empty array if the file does not exist.
+ *
+ * @example
+ * ```typescript
+ * const entries = await readManifest('/project');
+ * ```
+ *
  * @task T4465
  */
 export declare function readManifest(cwd?: string): Promise<ManifestEntry[]>;
 /**
  * Append a manifest entry.
+ *
+ * @param entry - The ManifestEntry to append
+ * @param cwd - Optional working directory for path resolution
+ *
+ * @remarks
+ * Appends a single JSON line to the MANIFEST.jsonl file.
+ *
+ * @example
+ * ```typescript
+ * await appendManifest({ id: 'M001', file: 'report.md', ... }, '/project');
+ * ```
+ *
  * @task T4465
  */
 export declare function appendManifest(entry: ManifestEntry, cwd?: string): Promise<void>;
 /**
- * Query manifest entries.
+ * Query manifest entries with filtering.
+ *
+ * @param options - Filter criteria (status, agentType, topic, taskId, limit)
+ * @param cwd - Optional working directory for path resolution
+ * @returns Filtered array of ManifestEntry records
+ *
+ * @remarks
+ * Applies filters sequentially: status, agentType, topic, taskId, then limit.
+ * Returns all entries when no filters are provided.
+ *
+ * @example
+ * ```typescript
+ * const entries = await queryManifest({ status: 'completed', limit: 5 }, '/project');
+ * ```
+ *
  * @task T4465
  */
 export declare function queryManifest(options?: ManifestQueryOptions, cwd?: string): Promise<ManifestEntry[]>;
 /** Extended manifest entry with optional fields used by the engine. */
 export interface ExtendedManifestEntry extends ManifestEntry {
+    /** Confidence score for the research findings. */
     confidence?: number;
+    /** SHA checksum of the output file. */
     file_checksum?: string;
+    /** Duration of the research in seconds. */
     duration_seconds?: number;
 }
 /** Research filter criteria used by the engine. */
 export interface ResearchFilter {
+    /** Filter by linked task ID. */
     taskId?: string;
+    /** Filter by completion status. */
     status?: string;
+    /** Filter by agent type. */
     agent_type?: string;
+    /** Filter by topic tag. */
     topic?: string;
+    /** Maximum entries to return. */
     limit?: number;
+    /** Number of entries to skip before applying limit. */
     offset?: number;
+    /** Filter by actionable flag. */
     actionable?: boolean;
+    /** Filter entries created after this ISO date. */
     dateAfter?: string;
+    /** Filter entries created before this ISO date. */
     dateBefore?: string;
 }
 /**
  * Read all manifest entries as extended entries.
+ *
+ * @param cwd - Optional working directory for path resolution
+ * @returns Array of parsed ExtendedManifestEntry records
+ *
+ * @remarks
+ * Same as readManifest but typed as ExtendedManifestEntry to include
+ * optional engine fields (confidence, file_checksum, duration_seconds).
+ *
+ * @example
+ * ```typescript
+ * const entries = await readExtendedManifest('/project');
+ * ```
+ *
  * @task T4787
  */
 export declare function readExtendedManifest(cwd?: string): Promise<ExtendedManifestEntry[]>;
 /**
  * Filter manifest entries by criteria.
+ *
+ * @param entries - Array of manifest entries to filter
+ * @param filter - Filter criteria to apply
+ * @returns Filtered subset of entries
+ *
+ * @remarks
+ * Applies filters in order: taskId, status, agent_type, topic, actionable,
+ * dateAfter, dateBefore, offset, then limit.
+ *
+ * @example
+ * ```typescript
+ * const filtered = filterManifestEntries(entries, { status: 'completed', limit: 10 });
+ * ```
+ *
  * @task T4787
  */
 export declare function filterManifestEntries(entries: ExtendedManifestEntry[], filter: ResearchFilter): ExtendedManifestEntry[];
 /**
  * Show a manifest entry by ID with optional file content.
+ *
+ * @param researchId - The manifest entry ID to look up
+ * @param cwd - Optional working directory for path resolution
+ * @returns The manifest entry with file content and existence flag
+ *
+ * @remarks
+ * Reads the output file referenced by the entry if it exists on disk.
+ * Throws CleoError NOT_FOUND if the entry ID is not found.
+ *
+ * @example
+ * ```typescript
+ * const entry = await showManifestEntry('T042-auth-research', '/project');
+ * if (entry.fileExists) console.log(entry.fileContent);
+ * ```
+ *
  * @task T4787
  */
 export declare function showManifestEntry(researchId: string, cwd?: string): Promise<ExtendedManifestEntry & {
@@ -164,6 +412,21 @@ export declare function showManifestEntry(researchId: string, cwd?: string): Pro
 }>;
 /**
  * Search manifest entries by text with relevance scoring.
+ *
+ * @param query - Text query to match against titles, topics, and findings
+ * @param options - Optional confidence threshold and limit
+ * @param cwd - Optional working directory for path resolution
+ * @returns Manifest entries with relevance scores, sorted by relevance descending
+ *
+ * @remarks
+ * Scores entries by matching against title (0.5), topics (0.3), key findings (0.2),
+ * and ID (0.1). Filters by minimum confidence threshold (default 0.1).
+ *
+ * @example
+ * ```typescript
+ * const results = await searchManifest('authentication', { limit: 5 }, '/project');
+ * ```
+ *
  * @task T4787
  */
 export declare function searchManifest(query: string, options?: {
@@ -174,6 +437,20 @@ export declare function searchManifest(query: string, options?: {
 }>>;
 /**
  * Get pending manifest entries (partial, blocked, or needing followup).
+ *
+ * @param epicId - Optional epic ID to scope results
+ * @param cwd - Optional working directory for path resolution
+ * @returns Pending entries with total count and status breakdown
+ *
+ * @remarks
+ * Includes entries with status "partial", "blocked", or any non-empty
+ * needs_followup array. Optionally scopes to entries linked to an epic.
+ *
+ * @example
+ * ```typescript
+ * const { entries, total } = await pendingManifestEntries('T001', '/project');
+ * ```
+ *
  * @task T4787
  */
 export declare function pendingManifestEntries(epicId?: string, cwd?: string): Promise<{
@@ -187,6 +464,21 @@ export declare function pendingManifestEntries(epicId?: string, cwd?: string): P
 }>;
 /**
  * Get manifest-based research statistics.
+ *
+ * @param epicId - Optional epic ID to scope statistics
+ * @param cwd - Optional working directory for path resolution
+ * @returns Totals, status/type distributions, actionable count, and average findings
+ *
+ * @remarks
+ * Aggregates manifest entries by status, agent type, and actionability.
+ * Calculates average key findings per entry.
+ *
+ * @example
+ * ```typescript
+ * const stats = await manifestStats(undefined, '/project');
+ * console.log(`${stats.total} entries, ${stats.actionable} actionable`);
+ * ```
+ *
  * @task T4787
  */
 export declare function manifestStats(epicId?: string, cwd?: string): Promise<{
@@ -199,6 +491,21 @@ export declare function manifestStats(epicId?: string, cwd?: string): Promise<{
 }>;
 /**
  * Link a manifest entry to a task (adds taskId to linked_tasks array).
+ *
+ * @param taskId - The task ID to link
+ * @param researchId - The manifest entry ID to link to
+ * @param cwd - Optional working directory for path resolution
+ * @returns Confirmation with link details and whether it was already linked
+ *
+ * @remarks
+ * Appends the taskId to the entry's linked_tasks array if not already present.
+ * Rewrites the entire MANIFEST.jsonl file after modification.
+ *
+ * @example
+ * ```typescript
+ * const result = await linkManifestEntry('T042', 'M001', '/project');
+ * ```
+ *
  * @task T4787
  */
 export declare function linkManifestEntry(taskId: string, researchId: string, cwd?: string): Promise<{
@@ -209,6 +516,20 @@ export declare function linkManifestEntry(taskId: string, researchId: string, cw
 /**
  * Append an extended manifest entry.
  * Validates required fields before appending.
+ *
+ * @param entry - The ExtendedManifestEntry to append
+ * @param cwd - Optional working directory for path resolution
+ * @returns Confirmation with the entry ID and manifest file path
+ *
+ * @remarks
+ * Validates that all required fields (id, file, title, date, status, agent_type,
+ * topics, actionable) are present before writing.
+ *
+ * @example
+ * ```typescript
+ * const result = await appendExtendedManifest({ id: 'M002', ... }, '/project');
+ * ```
+ *
  * @task T4787
  */
 export declare function appendExtendedManifest(entry: ExtendedManifestEntry, cwd?: string): Promise<{
@@ -217,6 +538,21 @@ export declare function appendExtendedManifest(entry: ExtendedManifestEntry, cwd
 }>;
 /**
  * Archive manifest entries older than a date.
+ *
+ * @param beforeDate - ISO date string; entries older than this are archived
+ * @param cwd - Optional working directory for path resolution
+ * @returns Counts of archived and remaining entries, and the archive file path
+ *
+ * @remarks
+ * Moves entries with a date before the threshold to MANIFEST.archive.jsonl
+ * and rewrites the main MANIFEST.jsonl with the remaining entries.
+ *
+ * @example
+ * ```typescript
+ * const result = await archiveManifestEntries('2026-01-01', '/project');
+ * console.log(`Archived ${result.archived} entries`);
+ * ```
+ *
  * @task T4787
  */
 export declare function archiveManifestEntries(beforeDate: string, cwd?: string): Promise<{
@@ -226,13 +562,31 @@ export declare function archiveManifestEntries(beforeDate: string, cwd?: string)
 }>;
 /** Contradiction detail between two manifest entries. */
 export interface ContradictionDetail {
+    /** First conflicting entry. */
     entryA: ExtendedManifestEntry;
+    /** Second conflicting entry. */
     entryB: ExtendedManifestEntry;
+    /** Shared topic where the conflict was detected. */
     topic: string;
+    /** Description of the conflicting findings. */
     conflictDetails: string;
 }
 /**
  * Find manifest entries with overlapping topics but conflicting key_findings.
+ *
+ * @param cwd - Optional working directory for path resolution
+ * @param params - Optional filter by topic
+ * @returns Array of contradiction details between conflicting entries
+ *
+ * @remarks
+ * Groups entries by shared topics and compares key_findings for disagreements.
+ * Only returns pairs where findings actually differ.
+ *
+ * @example
+ * ```typescript
+ * const contradictions = await findContradictions('/project', { topic: 'auth' });
+ * ```
+ *
  * @task T4787
  */
 export declare function findContradictions(cwd?: string, params?: {
@@ -246,6 +600,20 @@ export interface SupersededDetail {
 }
 /**
  * Identify research entries replaced by newer work on same topic.
+ *
+ * @param cwd - Optional working directory for path resolution
+ * @param params - Optional filter by topic
+ * @returns Array of superseded entry pairs with the replacement and obsoleted entries
+ *
+ * @remarks
+ * Groups entries by shared topics and identifies older entries that have been
+ * superseded by newer ones on the same subject.
+ *
+ * @example
+ * ```typescript
+ * const superseded = await findSuperseded('/project');
+ * ```
+ *
  * @task T4787
  */
 export declare function findSuperseded(cwd?: string, params?: {
@@ -253,6 +621,22 @@ export declare function findSuperseded(cwd?: string, params?: {
 }): Promise<SupersededDetail[]>;
 /**
  * Read protocol injection content for a given protocol type.
+ *
+ * @param protocolType - Protocol name (e.g. "consensus", "contribution")
+ * @param params - Optional parameters for template resolution
+ * @param cwd - Optional working directory for path resolution
+ * @returns Protocol content, file path, and metadata
+ *
+ * @remarks
+ * Reads protocol template files from the agent-outputs directory and
+ * resolves variables like taskId within the content.
+ *
+ * @example
+ * ```typescript
+ * const result = await readProtocolInjection('consensus', { taskId: 'T042' }, '/project');
+ * console.log(result.content);
+ * ```
+ *
  * @task T4787
  */
 export declare function readProtocolInjection(protocolType: string, params?: {
@@ -269,6 +653,20 @@ export declare function readProtocolInjection(protocolType: string, params?: {
 }>;
 /**
  * Compact MANIFEST.jsonl by removing duplicate/stale entries.
+ *
+ * @param cwd - Optional working directory for path resolution
+ * @returns Compaction summary with counts of removed entries
+ *
+ * @remarks
+ * Removes malformed lines and deduplicates entries by ID (keeping the last
+ * occurrence). Rewrites the file atomically.
+ *
+ * @example
+ * ```typescript
+ * const result = await compactManifest('/project');
+ * console.log(`Removed ${result.duplicatesRemoved} duplicates`);
+ * ```
+ *
  * @task T4787
  */
 export declare function compactManifest(cwd?: string): Promise<{
@@ -280,6 +678,21 @@ export declare function compactManifest(cwd?: string): Promise<{
 }>;
 /**
  * Validate research entries for a task.
+ *
+ * @param taskId - The task ID to validate manifest entries for
+ * @param cwd - Optional working directory for path resolution
+ * @returns Validation result with issue details and severity counts
+ *
+ * @remarks
+ * Checks linked manifest entries for missing output files, empty key findings,
+ * and incomplete status. Reports issues at error or warning severity.
+ *
+ * @example
+ * ```typescript
+ * const result = await validateManifestEntries('T042', '/project');
+ * if (!result.valid) console.log(result.issues);
+ * ```
+ *
  * @task T4787
  */
 export declare function validateManifestEntries(taskId: string, cwd?: string): Promise<{

package/dist/memory/index.d.ts.map

@@ -1 +1 @@
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