@cleocode/core 2026.4.9 → 2026.4.11

package/dist/memory/index.js

@@ -0,0 +1,1140 @@
+/**
+ * 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