@cleocode/core 2026.9.8 → 2026.9.10

package/dist/memory/manifest-ingestion.js

@@ -1,16 +1,15 @@
 /**
  * Ingestion functions for RCASD phase markdown and loose agent-output markdown
- * into pipeline_manifest table.
+ * into the canonical docs_pipeline_manifest table.
  *
  * @task T1099
  * @epic T1093 — MANIFEST/RCASD Architecture Unification
  * @spec T1096
  */
 import { createHash } from 'node:crypto';
-import { existsSync, readFileSync, statSync } from 'node:fs';
+import { readdirSync, readFileSync, statSync } from 'node:fs';
 import { join } from 'node:path';
-import { eq } from 'drizzle-orm';
-import { pipelineManifest } from '../store/tasks-schema.js';
+import { insertManifestRows } from './pipeline-manifest-sqlite.js';
 /**
  * Mapping from RCASD phase directory name to pipeline_manifest.type value.
  * Per T1096 §3.4.
@@ -108,261 +107,131 @@ function inferLooseFileType(filename) {
     // Fallback
     return 'implementation';
 }
+function readInputRoot(path) {
+    try {
+        return readdirSync(path);
+    }
+    catch (error) {
+        if (error instanceof Error && 'code' in error && error.code === 'ENOENT')
+            return [];
+        throw error;
+    }
+}
 /**
- * Ingest RCASD phase directories into pipeline_manifest.
- *
- * Reads `.cleo/rcasd/<TaskID>/<phase>/*.md` files and inserts each as a
- * pipeline_manifest row with:
- * - task_id: extracted from parent directory name
- * - type: mapped from phase directory name per §3.4
- * - content: full file contents
- * - source_file: relative path from project root
- * - metadata_json: {phase, rcasd_origin: true, ...}
- *
- * Uses INSERT OR IGNORE on content_hash for idempotency.
+ * Ingest RCASD phase markdown into the selected project's canonical manifest.
  *
- * @param projectRoot - absolute path to project root
- * @param db - Drizzle ORM database instance
- * @returns {ingested, skipped}
+ * @remarks
+ * Reads `.cleo/rcasd/<TaskID>/<phase>/*.md` without rewriting source content.
+ * The entire prepared batch commits atomically. Only identical persisted payloads
+ * are skipped; changed identities and legacy evidence require explicit repair.
+ * @param projectRoot - Explicit project directory owning the input and database.
+ * @param db - Caller-owned canonical task-domain database for that project.
+ * @returns Counts of inserted and identical existing entries.
+ * @throws If source reads, database ownership, history checks, or writes fail.
+ * @example
+ * ```ts
+ * const result = await ingestRcasdDirectories(projectRoot, db);
+ * ```
  */
 export async function ingestRcasdDirectories(projectRoot, db) {
     const rcasdRoot = join(projectRoot, '.cleo', 'rcasd');
-    let ingested = 0;
-    let skipped = 0;
-    // Check if rcasd directory exists
-    if (!existsSync(rcasdRoot)) {
-        return { ingested: 0, skipped: 0 };
-    }
-    // Read task directories
-    let taskDirs;
-    try {
-        const fs = await import('node:fs');
-        taskDirs = fs.readdirSync(rcasdRoot).filter((f) => {
-            const fullPath = join(rcasdRoot, f);
-            return fs.statSync(fullPath).isDirectory();
-        });
-    }
-    catch {
-        return { ingested: 0, skipped: 0 };
-    }
-    for (const taskDir of taskDirs) {
-        const taskId = taskDir; // e.g., T091
-        const taskPath = join(rcasdRoot, taskDir);
-        // Read phase subdirectories
-        let phaseDirs;
-        try {
-            const fs = await import('node:fs');
-            phaseDirs = fs.readdirSync(taskPath).filter((f) => {
-                const fullPath = join(taskPath, f);
-                return fs.statSync(fullPath).isDirectory();
-            });
-        }
-        catch {
-            continue;
-        }
+    const rows = [];
+    const taskDirs = readInputRoot(rcasdRoot).filter((name) => statSync(join(rcasdRoot, name)).isDirectory());
+    for (const taskId of taskDirs) {
+        const taskPath = join(rcasdRoot, taskId);
+        const phaseDirs = readdirSync(taskPath).filter((name) => statSync(join(taskPath, name)).isDirectory());
         for (const phaseDir of phaseDirs) {
             const phasePath = join(taskPath, phaseDir);
-            // Read markdown files in phase directory
-            let mdFiles;
-            try {
-                const fs = await import('node:fs');
-                mdFiles = fs.readdirSync(phasePath).filter((f) => f.endsWith('.md'));
-            }
-            catch {
-                continue;
-            }
-            for (const mdFile of mdFiles) {
+            for (const mdFile of readdirSync(phasePath).filter((name) => name.endsWith('.md'))) {
                 const filePath = join(phasePath, mdFile);
-                let content;
-                let mtime;
-                try {
-                    content = readFileSync(filePath, 'utf-8');
-                    const stat = statSync(filePath);
-                    mtime = new Date(stat.mtime);
-                }
-                catch {
-                    skipped++;
-                    continue;
-                }
-                // Generate manifest entry
-                const slug = stringToSlug(mdFile.replace(/\.md$/, ''));
-                const id = `${taskId}-rcasd-${phaseDir}-${slug}`;
-                const contentHash = computeContentHash(content);
-                const sourceFile = join('.cleo', 'rcasd', taskId, phaseDir, mdFile);
-                const createdAt = mtime.toISOString();
-                // Determine type from phase directory
-                const type = PHASE_TO_TYPE[phaseDir] || 'implementation';
-                // Prepare metadata
-                const metadataJson = {
+                const content = readFileSync(filePath, 'utf-8');
+                const metadata = {
                     phase: phaseDir,
                     rcasd_origin: true,
+                    ...((phaseDir === 'consensus' && mdFile === 'auto-complete-policy.md') ||
+                        (phaseDir === 'decomposition' && mdFile === 'worker-specs.md')
+                        ? { filename_note: 'non-T-prefixed or generic filename' }
+                        : {}),
+                    ...(phaseDir === 'decomposition' &&
+                        mdFile === 'T1008-worker-spec.md' &&
+                        taskId === 'T1007'
+                        ? { cross_task_ref: 'T1008' }
+                        : {}),
                 };
-                // Handle atypical files per §3.5
-                if ((phaseDir === 'consensus' && mdFile === 'auto-complete-policy.md') ||
-                    (phaseDir === 'decomposition' && mdFile === 'worker-specs.md')) {
-                    metadataJson.filename_note =
-                        'non-T-prefixed or generic filename';
-                }
-                if (phaseDir === 'decomposition' &&
-                    mdFile === 'T1008-worker-spec.md' &&
-                    taskId === 'T1007') {
-                    metadataJson.cross_task_ref = 'T1008';
-                }
-                // Insert into pipeline_manifest, skipping if already exists
-                try {
-                    // Check if this ID already exists (idempotency)
-                    const existing = await db
-                        .select({ id: pipelineManifest.id })
-                        .from(pipelineManifest)
-                        .where(eq(pipelineManifest.id, id))
-                        .limit(1);
-                    if (existing.length > 0) {
-                        // Already ingested, skip
-                        skipped++;
-                    }
-                    else {
-                        // Insert new entry
-                        await db.insert(pipelineManifest).values({
-                            id,
-                            taskId,
-                            epicId: null,
-                            sessionId: null,
-                            type,
-                            content,
-                            contentHash,
-                            status: 'active',
-                            distilled: false,
-                            brainObsId: null,
-                            sourceFile,
-                            metadataJson: JSON.stringify(metadataJson),
-                            createdAt,
-                            archivedAt: null,
-                        });
-                        ingested++;
-                    }
-                }
-                catch (err) {
-                    // Log but continue
-                    console.error(`Failed to ingest ${id}:`, err);
-                    skipped++;
-                }
+                rows.push({
+                    id: `${taskId}-rcasd-${phaseDir}-${stringToSlug(mdFile.replace(/\.md$/, ''))}`,
+                    sessionId: null,
+                    taskId,
+                    epicId: null,
+                    type: PHASE_TO_TYPE[phaseDir] || 'implementation',
+                    content,
+                    contentHash: computeContentHash(content),
+                    status: 'active',
+                    distilled: false,
+                    brainObsId: null,
+                    sourceFile: join('.cleo', 'rcasd', taskId, phaseDir, mdFile),
+                    metadataJson: JSON.stringify(metadata),
+                    createdAt: statSync(filePath).mtime.toISOString(),
+                    archivedAt: null,
+                });
             }
         }
     }
-    return { ingested, skipped };
+    const ingested = await insertManifestRows(rows, projectRoot, db);
+    return { ingested, skipped: rows.length - ingested };
 }
 /**
- * Ingest loose agent-output markdown files into pipeline_manifest.
+ * Ingest top-level agent-output markdown into the canonical manifest atomically.
  *
- * Reads `.cleo/agent-outputs/*.md` (maxdepth=1, no subdirectory recursion) and
- * inserts each as a pipeline_manifest row with:
- * - task_id: extracted from filename using T\d+ pattern, or null
- * - type: inferred from filename per §4.3 and overrides
- * - content: full file contents
- * - source_file: relative path: `.cleo/agent-outputs/<filename>`
- * - metadata_json: {loose_origin: true, original_filename, ...}
- *
- * Uses INSERT OR IGNORE on content_hash for idempotency.
- *
- * @param projectRoot - absolute path to project root
- * @param db - Drizzle ORM database instance
- * @returns {ingested, skipped}
+ * @remarks
+ * Reads `.cleo/agent-outputs/*.md` without descending into subdirectories.
+ * Preserves original content, source path, timestamp, and filename-derived metadata.
+ * Missing input directories are empty inputs; read and write failures propagate.
+ * @param projectRoot - Explicit project directory owning the input and database.
+ * @param db - Caller-owned canonical task-domain database for that project.
+ * @returns Counts of inserted and identical existing entries.
+ * @throws If source reads, database ownership, history checks, or writes fail.
+ * @example
+ * ```ts
+ * const result = await ingestLooseAgentOutputs(projectRoot, db);
+ * ```
  */
 export async function ingestLooseAgentOutputs(projectRoot, db) {
-    const agentOutputDir = join(projectRoot, '.cleo', 'agent-outputs');
-    let ingested = 0;
-    let skipped = 0;
-    // Check if agent-outputs directory exists
-    if (!existsSync(agentOutputDir)) {
-        return { ingested: 0, skipped: 0 };
-    }
-    // Read markdown files at maxdepth 1
-    let mdFiles;
-    try {
-        const fs = await import('node:fs');
-        mdFiles = fs.readdirSync(agentOutputDir).filter((f) => {
-            const fullPath = join(agentOutputDir, f);
-            const stat = fs.statSync(fullPath);
-            return stat.isFile() && f.endsWith('.md');
-        });
-    }
-    catch {
-        return { ingested: 0, skipped: 0 };
-    }
-    for (const mdFile of mdFiles) {
-        const filePath = join(agentOutputDir, mdFile);
-        let content;
-        let mtime;
-        try {
-            content = readFileSync(filePath, 'utf-8');
-            const stat = statSync(filePath);
-            mtime = new Date(stat.mtime);
-        }
-        catch {
-            skipped++;
+    const inputRoot = join(projectRoot, '.cleo', 'agent-outputs');
+    const rows = [];
+    for (const mdFile of readInputRoot(inputRoot)) {
+        const filePath = join(inputRoot, mdFile);
+        const stat = statSync(filePath);
+        if (!stat.isFile() || !mdFile.endsWith('.md'))
             continue;
-        }
-        // Extract task ID (may be null)
+        const content = readFileSync(filePath, 'utf-8');
         const taskId = extractTaskId(mdFile);
-        // Infer type from filename
-        const type = inferLooseFileType(mdFile);
-        // Generate ID
         const slug = stringToSlug(mdFile.replace(/\.md$/, ''));
-        const id = taskId ? `${taskId}-loose-${slug}` : `loose-${slug}`;
-        const contentHash = computeContentHash(content);
-        const sourceFile = join('.cleo', 'agent-outputs', mdFile);
-        const createdAt = mtime.toISOString();
-        // Prepare metadata
-        const metadataJson = {
-            loose_origin: true,
-            original_filename: mdFile,
-        };
-        // Tag flat RCASD phase files per §4.6
         const isRcasdPhase = taskId &&
             /^T\d+-(R\d+|CA\d+|[a-z-]+)-(.*)\.(md)$/i.test(mdFile) &&
-            FILENAME_TYPE_PATTERNS.some(([pat]) => pat.test(mdFile));
-        if (isRcasdPhase) {
-            metadataJson.flat_rcasd = true;
-        }
-        // Insert into pipeline_manifest, skipping if already exists
-        try {
-            // Check if this ID already exists (idempotency)
-            const existing = await db
-                .select({ id: pipelineManifest.id })
-                .from(pipelineManifest)
-                .where(eq(pipelineManifest.id, id))
-                .limit(1);
-            if (existing.length > 0) {
-                // Already ingested, skip
-                skipped++;
-            }
-            else {
-                // Insert new entry
-                await db.insert(pipelineManifest).values({
-                    id,
-                    taskId: taskId ?? null,
-                    epicId: null,
-                    sessionId: null,
-                    type,
-                    content,
-                    contentHash,
-                    status: 'active',
-                    distilled: false,
-                    brainObsId: null,
-                    sourceFile,
-                    metadataJson: JSON.stringify(metadataJson),
-                    createdAt,
-                    archivedAt: null,
-                });
-                ingested++;
-            }
-        }
-        catch (err) {
-            // Log but continue
-            console.error(`Failed to ingest ${id}:`, err);
-            skipped++;
-        }
+            FILENAME_TYPE_PATTERNS.some(([pattern]) => pattern.test(mdFile));
+        rows.push({
+            id: taskId ? `${taskId}-loose-${slug}` : `loose-${slug}`,
+            sessionId: null,
+            taskId,
+            epicId: null,
+            type: inferLooseFileType(mdFile),
+            content,
+            contentHash: computeContentHash(content),
+            status: 'active',
+            distilled: false,
+            brainObsId: null,
+            sourceFile: join('.cleo', 'agent-outputs', mdFile),
+            metadataJson: JSON.stringify({
+                loose_origin: true,
+                original_filename: mdFile,
+                ...(isRcasdPhase ? { flat_rcasd: true } : {}),
+            }),
+            createdAt: stat.mtime.toISOString(),
+            archivedAt: null,
+        });
     }
-    return { ingested, skipped };
+    const ingested = await insertManifestRows(rows, projectRoot, db);
+    return { ingested, skipped: rows.length - ingested };
 }
 //# sourceMappingURL=manifest-ingestion.js.map

package/dist/memory/manifest-ingestion.js.map

@@ -1 +1 @@
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package/dist/memory/observer-reflector.d.ts

@@ -94,6 +94,8 @@ export interface ReflectorResult {
     patternsStored: number;
     /** Number of new learnings stored. */
     learningsStored: number;
+    /** Candidate observation IDs that require sourced review before replacement. */
+    proposedSupersededIds?: string[];
     /** IDs of observations marked as superseded. */
     supersededIds: string[];
 }

package/dist/memory/observer-reflector.d.ts.map

@@ -1 +1 @@
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package/dist/memory/observer-reflector.js

@@ -319,34 +319,6 @@ function storeObserverNote(projectRoot, note, sessionId) {
         return null;
     }
 }
-/**
- * Mark observations as superseded by the reflector.
- * Sets invalid_at so they are excluded from future queries.
- */
-function markSuperseded(ids) {
-    if (ids.length === 0)
-        return;
-    const nativeDb = getBrainNativeDb();
-    if (!nativeDb)
-        return;
-    const now = new Date().toISOString().replace('T', ' ').slice(0, 19);
-    try {
-        // SQLite placeholder limit is 999; process in safe batches
-        const BATCH = 100;
-        for (let i = 0; i < ids.length; i += BATCH) {
-            const batch = ids.slice(i, i + BATCH);
-            const placeholders = batch.map(() => '?').join(',');
-            nativeDb
-                .prepare(`UPDATE brain_observations
-           SET invalid_at = ?, updated_at = ?
-           WHERE id IN (${placeholders}) AND invalid_at IS NULL`)
-                .run(now, now, ...batch);
-        }
-    }
-    catch {
-        /* best-effort */
-    }
-}
 // ============================================================================
 // Observer
 // ============================================================================
@@ -563,20 +535,18 @@ export async function runReflector(projectRoot, sessionId) {
     let learningsStored = 0;
     // T742: Collect IDs of newly stored patterns/learnings so we can write
     // supersedes graph edges from them to the superseded source observations.
-    const newEntryIds = [];
     // Store patterns
     if (Array.isArray(output.patterns)) {
         for (const p of output.patterns) {
             if (typeof p.pattern !== 'string' || !p.pattern)
                 continue;
             try {
-                const stored = await storePattern(projectRoot, {
+                await storePattern(projectRoot, {
                     type: 'workflow',
                     pattern: p.pattern.slice(0, 500),
                     context: (p.context ?? '').slice(0, 200),
                     source: REFLECTOR_SOURCE,
                 });
-                newEntryIds.push(`pattern:${stored.id}`);
                 patternsStored++;
             }
             catch {
@@ -591,13 +561,12 @@ export async function runReflector(projectRoot, sessionId) {
                 continue;
             const confidence = typeof l.confidence === 'number' ? Math.max(0.1, Math.min(1.0, l.confidence)) : 0.7;
             try {
-                const stored = await storeLearning(projectRoot, {
+                await storeLearning(projectRoot, {
                     insight: l.insight.slice(0, 500),
                     source: REFLECTOR_SOURCE,
                     confidence,
                     actionable: confidence >= 0.7,
                 });
-                newEntryIds.push(`learning:${stored.id}`);
                 learningsStored++;
             }
             catch {
@@ -605,29 +574,17 @@ export async function runReflector(projectRoot, sessionId) {
             }
         }
     }
-    // Mark superseded observations as invalid (soft-evict).
-    const supersededIds = Array.isArray(output.superseded)
+    // LLM synthesis cannot establish that source observations ceased to be true.
+    const proposedSupersededIds = Array.isArray(output.superseded)
         ? output.superseded.filter((id) => typeof id === 'string')
         : [];
-    markSuperseded(supersededIds);
-    // T742: Write supersedes graph edges from each new entry to each superseded
-    // observation. This links the synthesized knowledge back to its source
-    // observations in brain_page_edges so the supersession chain is traversable.
-    // All edge writes are best-effort — never block the return.
-    if (newEntryIds.length > 0 && supersededIds.length > 0) {
-        for (const newNodeId of newEntryIds) {
-            for (const obsId of supersededIds) {
-                addGraphEdge(projectRoot, newNodeId, `observation:${obsId}`, 'supersedes', 1.0, 'reflector-synthesized:session-end-reflection').catch(() => {
-                    /* best-effort */
-                });
-            }
-        }
-    }
+    const supersededIds = [];
     return {
         ran: true,
         patternsStored,
         learningsStored,
         supersededIds,
+        proposedSupersededIds,
     };
 }
 //# sourceMappingURL=observer-reflector.js.map

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package/dist/memory/patterns.d.ts

@@ -48,6 +48,16 @@ export interface SearchPatternParams {
 /**
  * Store a new pattern.
  * If a similar pattern already exists (same type + matching text), increments frequency.
+ * @param projectRoot - Explicit owning project root captured before asynchronous work.
+ * @param params - Existing pattern fields and extraction-gate policy.
+ * @returns The stored or merged pattern; graph projection remains an optional tracked effect.
+ * @remarks Both graph branches retain the original execution context and completion
+ * barrier. Cancellation after a pattern commit can prevent graph projection without
+ * undoing the committed pattern. Scoped primary writes share the same original fence.
+ * @example
+ * ```ts
+ * await storePattern(root, { type: 'workflow', pattern: 'Run tests', context: 'Before release' });
+ * ```
  * @task T4768, T5241
  */
 export declare function storePattern(projectRoot: string, params: StorePatternParams): Promise<{