@cleocode/core 2026.4.13 → 2026.4.15

package/dist/memory/index.js

@@ -1,1140 +0,0 @@
-/**
- * Research commands and manifest operations.
- *
- * @packageDocumentation
- * @task T4465
- * @epic T4454
- */
-import { existsSync, readFileSync } from 'node:fs';
-import { join, resolve } from 'node:path';
-import { ExitCode } from '@cleocode/contracts';
-import { CleoError } from '../errors.js';
-import { getBackupDir, getManifestPath as getCentralManifestPath, getCleoDirAbsolute, getManifestArchivePath, getProjectRoot, } from '../paths.js';
-import { atomicWrite, safeReadFile } from '../store/atomic.js';
-import { appendJsonl, readJson, saveJson } from '../store/json.js';
-import { logOperation } from '../tasks/add.js';
-/**
- * Get the research file path.
- * @task T4465
- */
-function getResearchPath(cwd) {
-    return join(getCleoDirAbsolute(cwd), 'research.json');
-}
-/**
- * Get the manifest file path.
- * @task T4465
- */
-function getManifestPath(cwd) {
-    return getCentralManifestPath(cwd);
-}
-/**
- * Read or initialize the research file.
- * @task T4465
- */
-async function readResearch(cwd) {
-    const path = getResearchPath(cwd);
-    const data = await readJson(path);
-    return data ?? { entries: [] };
-}
-/**
- * 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 async function addResearch(options, cwd, accessor) {
-    // Validate task exists
-    const task = await accessor.loadSingleTask(options.taskId);
-    if (!task) {
-        throw new CleoError(ExitCode.NOT_FOUND, `Task not found: ${options.taskId}`);
-    }
-    if (!options.topic || options.topic.trim().length === 0) {
-        throw new CleoError(ExitCode.INVALID_INPUT, 'Research topic is required');
-    }
-    const research = await readResearch(cwd);
-    const now = new Date().toISOString();
-    const entry = {
-        id: `R${Date.now().toString(36)}`,
-        taskId: options.taskId,
-        topic: options.topic.trim(),
-        findings: options.findings ?? [],
-        sources: options.sources ?? [],
-        status: (options.findings?.length ?? 0) > 0 ? 'complete' : 'pending',
-        createdAt: now,
-        updatedAt: now,
-    };
-    research.entries.push(entry);
-    await saveJson(getResearchPath(cwd), research, { backupDir: getBackupDir(cwd) });
-    await logOperation('research_added', entry.id, {
-        taskId: options.taskId,
-        topic: options.topic,
-    }, accessor);
-    return entry;
-}
-/**
- * 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 async function showResearch(researchId, cwd) {
-    const research = await readResearch(cwd);
-    const entry = research.entries.find((e) => e.id === researchId);
-    if (!entry) {
-        throw new CleoError(ExitCode.NOT_FOUND, `Research entry not found: ${researchId}`);
-    }
-    return entry;
-}
-/**
- * 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 async function listResearch(options = {}, cwd) {
-    const research = await readResearch(cwd);
-    let entries = research.entries;
-    if (options.taskId) {
-        entries = entries.filter((e) => e.taskId === options.taskId);
-    }
-    if (options.status) {
-        entries = entries.filter((e) => e.status === options.status);
-    }
-    return entries;
-}
-/**
- * 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 async function pendingResearch(cwd) {
-    return listResearch({ status: 'pending' }, cwd);
-}
-/**
- * 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 async function linkResearch(researchId, taskId, cwd, accessor) {
-    const research = await readResearch(cwd);
-    const entry = research.entries.find((e) => e.id === researchId);
-    if (!entry) {
-        throw new CleoError(ExitCode.NOT_FOUND, `Research entry not found: ${researchId}`);
-    }
-    // Validate task exists
-    const linkedTask = await accessor.loadSingleTask(taskId);
-    if (!linkedTask) {
-        throw new CleoError(ExitCode.NOT_FOUND, `Task not found: ${taskId}`);
-    }
-    entry.taskId = taskId;
-    entry.updatedAt = new Date().toISOString();
-    await saveJson(getResearchPath(cwd), research, { backupDir: getBackupDir(cwd) });
-    return { researchId, taskId };
-}
-/**
- * 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 async function updateResearch(researchId, updates, cwd) {
-    const research = await readResearch(cwd);
-    const entry = research.entries.find((e) => e.id === researchId);
-    if (!entry) {
-        throw new CleoError(ExitCode.NOT_FOUND, `Research entry not found: ${researchId}`);
-    }
-    if (updates.findings)
-        entry.findings = updates.findings;
-    if (updates.sources)
-        entry.sources = updates.sources;
-    if (updates.status)
-        entry.status = updates.status;
-    entry.updatedAt = new Date().toISOString();
-    await saveJson(getResearchPath(cwd), research, { backupDir: getBackupDir(cwd) });
-    return entry;
-}
-/**
- * Get research statistics.
- *
- * @param cwd - Optional working directory for path resolution
- * @returns Total count and breakdowns by status and topic
- *
- * @remarks
- * Aggregates all research entries into status and topic distributions.
- *
- * @example
- * ```typescript
- * const stats = await statsResearch('/project');
- * console.log(`${stats.total} entries, ${stats.byStatus.pending ?? 0} pending`);
- * ```
- *
- * @task T4474
- */
-export async function statsResearch(cwd) {
-    const research = await readResearch(cwd);
-    const byStatus = {};
-    const byTopic = {};
-    for (const entry of research.entries) {
-        byStatus[entry.status] = (byStatus[entry.status] || 0) + 1;
-        byTopic[entry.topic] = (byTopic[entry.topic] || 0) + 1;
-    }
-    return {
-        total: research.entries.length,
-        byStatus,
-        byTopic,
-    };
-}
-/**
- * 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 async function linksResearch(taskId, cwd) {
-    if (!taskId) {
-        throw new CleoError(ExitCode.INVALID_INPUT, 'Task ID is required');
-    }
-    const research = await readResearch(cwd);
-    return research.entries.filter((e) => e.taskId === taskId);
-}
-/**
- * Archive old research entries by status.
- * 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 async function archiveResearch(cwd) {
-    const research = await readResearch(cwd);
-    const completed = research.entries.filter((e) => e.status === 'complete');
-    const remaining = research.entries.filter((e) => e.status !== 'complete');
-    // Write back only non-complete entries
-    await saveJson(getResearchPath(cwd), { entries: remaining }, { backupDir: getBackupDir(cwd) });
-    return {
-        action: 'archive',
-        entriesArchived: completed.length,
-        entriesRemaining: remaining.length,
-    };
-}
-// === MANIFEST OPERATIONS ===
-/**
- * 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 async function readManifest(cwd) {
-    const manifestPath = getManifestPath(cwd);
-    const content = await safeReadFile(manifestPath);
-    if (!content)
-        return [];
-    const entries = [];
-    for (const line of content.split('\n')) {
-        const trimmed = line.trim();
-        if (!trimmed)
-            continue;
-        try {
-            entries.push(JSON.parse(trimmed));
-        }
-        catch {
-            // Skip malformed lines
-        }
-    }
-    return entries;
-}
-/**
- * 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 async function appendManifest(entry, cwd) {
-    const manifestPath = getManifestPath(cwd);
-    await appendJsonl(manifestPath, entry);
-}
-/**
- * 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 async function queryManifest(options = {}, cwd) {
-    let entries = await readManifest(cwd);
-    if (options.status) {
-        entries = entries.filter((e) => e.status === options.status);
-    }
-    if (options.agentType) {
-        entries = entries.filter((e) => e.agent_type === options.agentType);
-    }
-    if (options.topic) {
-        entries = entries.filter((e) => e.topics.includes(options.topic));
-    }
-    if (options.taskId) {
-        entries = entries.filter((e) => e.linked_tasks.includes(options.taskId));
-    }
-    if (options.limit && options.limit > 0) {
-        entries = entries.slice(0, options.limit);
-    }
-    return entries;
-}
-/**
- * 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 async function readExtendedManifest(cwd) {
-    const manifestPath = getManifestPath(cwd);
-    const content = await safeReadFile(manifestPath);
-    if (!content)
-        return [];
-    const entries = [];
-    for (const line of content.split('\n')) {
-        const trimmed = line.trim();
-        if (!trimmed)
-            continue;
-        try {
-            entries.push(JSON.parse(trimmed));
-        }
-        catch {
-            // Skip malformed lines
-        }
-    }
-    return entries;
-}
-/**
- * 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 function filterManifestEntries(entries, filter) {
-    let filtered = entries;
-    if (filter.taskId) {
-        const taskId = filter.taskId;
-        filtered = filtered.filter((e) => e.id.startsWith(taskId) || e.linked_tasks?.includes(taskId));
-    }
-    if (filter.status) {
-        filtered = filtered.filter((e) => e.status === filter.status);
-    }
-    if (filter.agent_type) {
-        filtered = filtered.filter((e) => e.agent_type === filter.agent_type);
-    }
-    if (filter.topic) {
-        filtered = filtered.filter((e) => e.topics.includes(filter.topic));
-    }
-    if (filter.actionable !== undefined) {
-        filtered = filtered.filter((e) => e.actionable === filter.actionable);
-    }
-    if (filter.dateAfter) {
-        filtered = filtered.filter((e) => e.date > filter.dateAfter);
-    }
-    if (filter.dateBefore) {
-        filtered = filtered.filter((e) => e.date < filter.dateBefore);
-    }
-    if (filter.offset && filter.offset > 0) {
-        filtered = filtered.slice(filter.offset);
-    }
-    if (filter.limit && filter.limit > 0) {
-        filtered = filtered.slice(0, filter.limit);
-    }
-    return filtered;
-}
-/**
- * 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 async function showManifestEntry(researchId, cwd) {
-    const entries = await readExtendedManifest(cwd);
-    const entry = entries.find((e) => e.id === researchId);
-    if (!entry) {
-        throw new CleoError(ExitCode.NOT_FOUND, `Research entry '${researchId}' not found`);
-    }
-    const root = getProjectRoot(cwd);
-    let fileContent = null;
-    try {
-        const filePath = resolve(root, entry.file);
-        if (existsSync(filePath)) {
-            fileContent = readFileSync(filePath, 'utf-8');
-        }
-    }
-    catch {
-        // File may not exist or be unreadable
-    }
-    return {
-        ...entry,
-        fileContent,
-        fileExists: fileContent !== null,
-    };
-}
-/**
- * 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 async function searchManifest(query, options, cwd) {
-    const entries = await readExtendedManifest(cwd);
-    const queryLower = query.toLowerCase();
-    const scored = entries.map((entry) => {
-        let score = 0;
-        if (entry.title.toLowerCase().includes(queryLower)) {
-            score += 0.5;
-        }
-        if (entry.topics.some((t) => t.toLowerCase().includes(queryLower))) {
-            score += 0.3;
-        }
-        if (entry.key_findings?.some((f) => f.toLowerCase().includes(queryLower))) {
-            score += 0.2;
-        }
-        if (entry.id.toLowerCase().includes(queryLower)) {
-            score += 0.1;
-        }
-        return { entry, score };
-    });
-    const minConfidence = options?.confidence ?? 0.1;
-    let results = scored.filter((s) => s.score >= minConfidence).sort((a, b) => b.score - a.score);
-    if (options?.limit && options.limit > 0) {
-        results = results.slice(0, options.limit);
-    }
-    return results.map((r) => ({
-        ...r.entry,
-        relevanceScore: Math.round(r.score * 100) / 100,
-    }));
-}
-/**
- * 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 async function pendingManifestEntries(epicId, cwd) {
-    const entries = await readExtendedManifest(cwd);
-    let pending = entries.filter((e) => e.status === 'partial' ||
-        e.status === 'blocked' ||
-        (e.needs_followup && e.needs_followup.length > 0));
-    if (epicId) {
-        pending = pending.filter((e) => e.id.startsWith(epicId) || e.linked_tasks?.includes(epicId));
-    }
-    return {
-        entries: pending,
-        total: pending.length,
-        byStatus: {
-            partial: pending.filter((e) => e.status === 'partial').length,
-            blocked: pending.filter((e) => e.status === 'blocked').length,
-            needsFollowup: pending.filter((e) => e.needs_followup && e.needs_followup.length > 0).length,
-        },
-    };
-}
-/**
- * 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 async function manifestStats(epicId, cwd) {
-    const entries = await readExtendedManifest(cwd);
-    let filtered = entries;
-    if (epicId) {
-        filtered = entries.filter((e) => e.id.startsWith(epicId) || e.linked_tasks?.includes(epicId));
-    }
-    const byStatus = {};
-    const byType = {};
-    let actionable = 0;
-    let needsFollowup = 0;
-    let totalFindings = 0;
-    for (const entry of filtered) {
-        byStatus[entry.status] = (byStatus[entry.status] || 0) + 1;
-        byType[entry.agent_type] = (byType[entry.agent_type] || 0) + 1;
-        if (entry.actionable)
-            actionable++;
-        if (entry.needs_followup && entry.needs_followup.length > 0)
-            needsFollowup++;
-        if (entry.key_findings)
-            totalFindings += entry.key_findings.length;
-    }
-    return {
-        total: filtered.length,
-        byStatus,
-        byType,
-        actionable,
-        needsFollowup,
-        averageFindings: filtered.length > 0 ? Math.round((totalFindings / filtered.length) * 10) / 10 : 0,
-    };
-}
-/**
- * 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 async function linkManifestEntry(taskId, researchId, cwd) {
-    const manifestPath = getManifestPath(cwd);
-    const entries = await readExtendedManifest(cwd);
-    const entryIndex = entries.findIndex((e) => e.id === researchId);
-    if (entryIndex === -1) {
-        throw new CleoError(ExitCode.NOT_FOUND, `Research entry '${researchId}' not found`);
-    }
-    const entry = entries[entryIndex];
-    if (entry.linked_tasks?.includes(taskId)) {
-        return { taskId, researchId, alreadyLinked: true };
-    }
-    if (!entry.linked_tasks) {
-        entry.linked_tasks = [];
-    }
-    entry.linked_tasks.push(taskId);
-    const content = entries.map((e) => JSON.stringify(e)).join('\n') + '\n';
-    await atomicWrite(manifestPath, content);
-    return { taskId, researchId, alreadyLinked: false };
-}
-/**
- * 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 async function appendExtendedManifest(entry, cwd) {
-    const errors = [];
-    if (!entry.id)
-        errors.push('id is required');
-    if (!entry.file)
-        errors.push('file is required');
-    if (!entry.title)
-        errors.push('title is required');
-    if (!entry.date)
-        errors.push('date is required');
-    if (!entry.status)
-        errors.push('status is required');
-    if (!entry.agent_type)
-        errors.push('agent_type is required');
-    if (!entry.topics)
-        errors.push('topics is required');
-    if (entry.actionable === undefined)
-        errors.push('actionable is required');
-    if (errors.length > 0) {
-        throw new CleoError(ExitCode.VALIDATION_ERROR, `Invalid manifest entry: ${errors.join(', ')}`);
-    }
-    const manifestPath = getManifestPath(cwd);
-    await appendJsonl(manifestPath, entry);
-    return { entryId: entry.id, file: getManifestPath() };
-}
-/**
- * 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 async function archiveManifestEntries(beforeDate, cwd) {
-    const manifestPath = getManifestPath(cwd);
-    const archivePath = getManifestArchivePath(cwd);
-    const entries = await readExtendedManifest(cwd);
-    const toArchive = entries.filter((e) => e.date < beforeDate);
-    const toKeep = entries.filter((e) => e.date >= beforeDate);
-    if (toArchive.length === 0) {
-        return {
-            archived: 0,
-            remaining: entries.length,
-            archiveFile: getManifestArchivePath(),
-        };
-    }
-    // Append archived entries to archive file
-    const existingArchive = await safeReadFile(archivePath);
-    const archiveContent = toArchive.map((e) => JSON.stringify(e)).join('\n') + '\n';
-    const fullArchive = existingArchive
-        ? existingArchive.trimEnd() + '\n' + archiveContent
-        : archiveContent;
-    await atomicWrite(archivePath, fullArchive);
-    // Rewrite main manifest with remaining entries
-    const remainingContent = toKeep.length > 0 ? toKeep.map((e) => JSON.stringify(e)).join('\n') + '\n' : '';
-    await atomicWrite(manifestPath, remainingContent);
-    return {
-        archived: toArchive.length,
-        remaining: toKeep.length,
-        archiveFile: getManifestArchivePath(),
-    };
-}
-/**
- * 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 async function findContradictions(cwd, params) {
-    const entries = await readExtendedManifest(cwd);
-    const byTopic = new Map();
-    for (const entry of entries) {
-        if (!entry.key_findings || entry.key_findings.length === 0)
-            continue;
-        for (const topic of entry.topics) {
-            if (params?.topic && topic !== params.topic)
-                continue;
-            if (!byTopic.has(topic)) {
-                byTopic.set(topic, []);
-            }
-            byTopic.get(topic).push(entry);
-        }
-    }
-    const contradictions = [];
-    const negationPairs = [
-        [/\bdoes NOT\b/i, /\bdoes\b(?!.*\bnot\b)/i],
-        [/\bcannot\b/i, /\bcan\b(?!.*\bnot\b)/i],
-        [/\bno\s+\w+\s+required\b/i, /\brequired\b(?!.*\bno\b)/i],
-        [
-            /\bnot\s+(?:available|supported|possible|recommended)\b/i,
-            /\b(?:available|supported|possible|recommended)\b(?!.*\bnot\b)/i,
-        ],
-        [/\bwithout\b/i, /\brequires?\b/i],
-        [/\bavoid\b/i, /\buse\b/i],
-        [/\bdeprecated\b/i, /\brecommended\b/i],
-        [/\banti-pattern\b/i, /\bbest practice\b/i],
-    ];
-    for (const [topic, topicEntries] of byTopic) {
-        if (topicEntries.length < 2)
-            continue;
-        for (let i = 0; i < topicEntries.length; i++) {
-            for (let j = i + 1; j < topicEntries.length; j++) {
-                const a = topicEntries[i];
-                const b = topicEntries[j];
-                const conflicts = [];
-                for (const findingA of a.key_findings) {
-                    for (const findingB of b.key_findings) {
-                        for (const [patternNeg, patternPos] of negationPairs) {
-                            if ((patternNeg.test(findingA) && patternPos.test(findingB)) ||
-                                (patternPos.test(findingA) && patternNeg.test(findingB))) {
-                                conflicts.push(`"${findingA}" vs "${findingB}"`);
-                                break;
-                            }
-                        }
-                    }
-                }
-                if (conflicts.length > 0) {
-                    contradictions.push({
-                        entryA: a,
-                        entryB: b,
-                        topic,
-                        conflictDetails: conflicts.join('; '),
-                    });
-                }
-            }
-        }
-    }
-    return contradictions;
-}
-/**
- * Identify research entries replaced by newer work on same topic.
- *
- * @param cwd - Optional working directory for path resolution
- * @param params - Optional filter by topic
- * @returns Array of superseded entry pairs with the replacement and obsoleted entries
- *
- * @remarks
- * Groups entries by shared topics and identifies older entries that have been
- * superseded by newer ones on the same subject.
- *
- * @example
- * ```typescript
- * const superseded = await findSuperseded('/project');
- * ```
- *
- * @task T4787
- */
-export async function findSuperseded(cwd, params) {
-    const entries = await readExtendedManifest(cwd);
-    const byTopicAndType = new Map();
-    for (const entry of entries) {
-        for (const topic of entry.topics) {
-            if (params?.topic && topic !== params.topic)
-                continue;
-            const key = `${topic}::${entry.agent_type}`;
-            if (!byTopicAndType.has(key)) {
-                byTopicAndType.set(key, []);
-            }
-            byTopicAndType.get(key).push(entry);
-        }
-    }
-    const superseded = [];
-    const seenPairs = new Set();
-    for (const [key, groupEntries] of byTopicAndType) {
-        if (groupEntries.length < 2)
-            continue;
-        const topic = key.split('::')[0];
-        const sorted = [...groupEntries].sort((a, b) => a.date.localeCompare(b.date));
-        for (let i = 0; i < sorted.length - 1; i++) {
-            const pairKey = `${sorted[i].id}::${sorted[sorted.length - 1].id}::${topic}`;
-            if (seenPairs.has(pairKey))
-                continue;
-            seenPairs.add(pairKey);
-            superseded.push({
-                old: sorted[i],
-                replacement: sorted[sorted.length - 1],
-                topic,
-            });
-        }
-    }
-    return superseded;
-}
-/**
- * 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 async function readProtocolInjection(protocolType, params, cwd) {
-    const root = getProjectRoot(cwd);
-    const protocolLocations = [
-        resolve(root, 'protocols', `${protocolType}.md`),
-        resolve(root, 'skills', '_shared', `${protocolType}.md`),
-        resolve(root, 'agents', 'cleo-subagent', 'protocols', `${protocolType}.md`),
-    ];
-    let protocolContent = null;
-    let protocolPath = null;
-    for (const loc of protocolLocations) {
-        if (existsSync(loc)) {
-            try {
-                protocolContent = readFileSync(loc, 'utf-8');
-                protocolPath = loc.replace(root + '/', '');
-                break;
-            }
-            catch { }
-        }
-    }
-    if (!protocolContent || !protocolPath) {
-        throw new CleoError(ExitCode.NOT_FOUND, `Protocol '${protocolType}' not found in src/protocols/, skills/_shared/, or agents/cleo-subagent/protocols/`);
-    }
-    return {
-        protocolType,
-        content: protocolContent,
-        path: protocolPath,
-        contentLength: protocolContent.length,
-        estimatedTokens: Math.ceil(protocolContent.length / 4),
-        taskId: params?.taskId || null,
-        variant: params?.variant || null,
-    };
-}
-/**
- * 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 async function compactManifest(cwd) {
-    const manifestPath = getManifestPath(cwd);
-    const content = await safeReadFile(manifestPath);
-    if (!content) {
-        return {
-            compacted: false,
-            originalLines: 0,
-            malformedRemoved: 0,
-            duplicatesRemoved: 0,
-            remainingEntries: 0,
-        };
-    }
-    const lines = content.split('\n');
-    const entries = [];
-    let malformedCount = 0;
-    for (const line of lines) {
-        const trimmed = line.trim();
-        if (!trimmed)
-            continue;
-        try {
-            entries.push(JSON.parse(trimmed));
-        }
-        catch {
-            malformedCount++;
-        }
-    }
-    const originalCount = entries.length + malformedCount;
-    const idMap = new Map();
-    for (const entry of entries) {
-        idMap.set(entry.id, entry);
-    }
-    const compacted = Array.from(idMap.values());
-    const duplicatesRemoved = entries.length - compacted.length;
-    const compactedContent = compacted.length > 0 ? compacted.map((e) => JSON.stringify(e)).join('\n') + '\n' : '';
-    await atomicWrite(manifestPath, compactedContent);
-    return {
-        compacted: true,
-        originalLines: originalCount,
-        malformedRemoved: malformedCount,
-        duplicatesRemoved,
-        remainingEntries: compacted.length,
-    };
-}
-/**
- * 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 async function validateManifestEntries(taskId, cwd) {
-    const root = getProjectRoot(cwd);
-    const entries = await readExtendedManifest(cwd);
-    const linked = entries.filter((e) => e.id.startsWith(taskId) || e.linked_tasks?.includes(taskId));
-    if (linked.length === 0) {
-        return {
-            taskId,
-            valid: true,
-            entriesFound: 0,
-            issues: [],
-            errorCount: 0,
-            warningCount: 0,
-        };
-    }
-    const issues = [];
-    for (const entry of linked) {
-        if (!entry.id)
-            issues.push({ entryId: entry.id || '(unknown)', issue: 'Missing id', severity: 'error' });
-        if (!entry.file)
-            issues.push({ entryId: entry.id, issue: 'Missing file path', severity: 'error' });
-        if (!entry.title)
-            issues.push({ entryId: entry.id, issue: 'Missing title', severity: 'error' });
-        if (!entry.date)
-            issues.push({ entryId: entry.id, issue: 'Missing date', severity: 'error' });
-        if (!entry.status)
-            issues.push({ entryId: entry.id, issue: 'Missing status', severity: 'error' });
-        if (!entry.agent_type)
-            issues.push({ entryId: entry.id, issue: 'Missing agent_type', severity: 'error' });
-        if (entry.status && !['completed', 'partial', 'blocked'].includes(entry.status)) {
-            issues.push({
-                entryId: entry.id,
-                issue: `Invalid status: ${entry.status}`,
-                severity: 'error',
-            });
-        }
-        if (entry.file) {
-            const filePath = resolve(root, entry.file);
-            if (!existsSync(filePath)) {
-                issues.push({
-                    entryId: entry.id,
-                    issue: `Output file not found: ${entry.file}`,
-                    severity: 'warning',
-                });
-            }
-        }
-        if (entry.agent_type === 'research' &&
-            (!entry.key_findings || entry.key_findings.length === 0)) {
-            issues.push({
-                entryId: entry.id,
-                issue: 'Research entry missing key_findings',
-                severity: 'warning',
-            });
-        }
-    }
-    return {
-        taskId,
-        valid: issues.filter((i) => i.severity === 'error').length === 0,
-        entriesFound: linked.length,
-        issues,
-        errorCount: issues.filter((i) => i.severity === 'error').length,
-        warningCount: issues.filter((i) => i.severity === 'warning').length,
-    };
-}
-// === BRAIN Lifecycle (temporal decay) ===
-export * from './brain-lifecycle.js';
-export * from './brain-links.js';
-export * from './brain-migration.js';
-// === BRAIN Retrieval functions (3-layer pattern) ===
-export * from './brain-retrieval.js';
-export * from './brain-search.js';
-// === BRAIN Memory modules (brain.db backed) ===
-export * from './decisions.js';
-export * from './learnings.js';
-// === JSONL Memory modules (legacy, still active) ===
-export * from './patterns.js';
-//# sourceMappingURL=index.js.map