@cleocode/core 2026.10.27 → 2026.11.1-canary.10

package/dist/memory/graph-memory-bridge.d.ts

@@ -278,34 +278,3 @@ export interface MemoryContextHit {
  * @epic T1081
  */
 export declare function queryMemoriesForContext(projectRoot: string, params?: MemoriesForContextParams): Promise<MemoryContextHit[]>;
-/**
- * Result from linkConduitMessagesToSymbols.
- */
-export interface ConduitSymbolLinkResult {
-    /** Number of new `conduit_mentions_symbol` edges created. */
-    linked: number;
-    /** Total messages scanned. */
-    scanned: number;
-}
-/**
- * Scan conduit.messages for symbol name mentions and link them to nexus_nodes.
- *
- * Scope per HITL-4:
- * - Query messages where `attachments != '[]'` OR `content` FTS5-matches symbol names
- * - Build symbolNames FTS query from top 200 nexus nodes (most plastically weighted)
- * - For each matched message, write `conduit_mentions_symbol` edges to brain_page_edges
- * - Idempotent via UNIQUE (source, target, type) constraint
- *
- * Gracefully no-ops if:
- * - conduit.db file does not exist (not initialized)
- * - nexus.db is unavailable
- *
- * All errors are caught and logged; never throws.
- *
- * @param projectRoot - Absolute path to project root (locates conduit.db)
- * @returns Summary of scanned messages and created edges
- * @task T1071
- * @epic T1042
- */
-export declare function linkConduitMessagesToSymbols(projectRoot: string): Promise<ConduitSymbolLinkResult>;
-//# sourceMappingURL=graph-memory-bridge.d.ts.map

package/dist/memory/graph-memory-bridge.js

@@ -17,19 +17,11 @@
  * @task graph-memory-bridge
  * @epic T523
  */
-import { existsSync } from 'node:fs';
-import { createRequire } from 'node:module';
-import { getConduitDbPath } from '../store/conduit-sqlite.js';
 import { getBrainDb, getBrainNativeDb } from '../store/memory-sqlite.js';
 import { getNexusDb, getNexusNativeDb } from '../store/nexus-sqlite.js';
 import { brainPageEdges, brainPageNodes } from '../store/schema/memory-schema.js';
-import { applyPerfPragmas } from '../store/sqlite-pragmas.js';
 import { typedAll } from '../store/typed-query.js';
-import { installSchemaWriteGuard } from '../store/worktree-build-guard.js';
-import { withWriterLease } from '../store/writer-lease.js';
 import { isCurrentDecisionCodeEvidence, linkDecisionToCodeEvidence, readDecisionCodeEvidence, } from './decision-cross-link.js';
-const _require = createRequire(import.meta.url);
-const { DatabaseSync } = _require('node:sqlite');
 // ---------------------------------------------------------------------------
 // Internal helpers
 // ---------------------------------------------------------------------------
@@ -913,158 +905,4 @@ export async function queryMemoriesForContext(projectRoot, params = {}) {
     }
     return hits;
 }
-/**
- * Scan conduit.messages for symbol name mentions and link them to nexus_nodes.
- *
- * Scope per HITL-4:
- * - Query messages where `attachments != '[]'` OR `content` FTS5-matches symbol names
- * - Build symbolNames FTS query from top 200 nexus nodes (most plastically weighted)
- * - For each matched message, write `conduit_mentions_symbol` edges to brain_page_edges
- * - Idempotent via UNIQUE (source, target, type) constraint
- *
- * Gracefully no-ops if:
- * - conduit.db file does not exist (not initialized)
- * - nexus.db is unavailable
- *
- * All errors are caught and logged; never throws.
- *
- * @param projectRoot - Absolute path to project root (locates conduit.db)
- * @returns Summary of scanned messages and created edges
- * @task T1071
- * @epic T1042
- */
-export async function linkConduitMessagesToSymbols(projectRoot) {
-    const result = { linked: 0, scanned: 0 };
-    try {
-        // Check if conduit.db exists
-        const conduitDbPath = getConduitDbPath(projectRoot);
-        if (!existsSync(conduitDbPath)) {
-            return result; // Graceful no-op
-        }
-        // Open conduit.db for this operation — apply pragma SSoT (T9023)
-        const conduitDb = new DatabaseSync(conduitDbPath); // db-open-allowed: hot-path conduit.db open with full pragma SSoT (T9023); core-owned conduit infrastructure
-        applyPerfPragmas(conduitDb); // hot-path; full pragma set (WAL, busy_timeout, cache)
-        installSchemaWriteGuard(conduitDb); // T12687
-        try {
-            // Ensure brain.db is available for edge writes
-            await getBrainDb(projectRoot);
-            const brainNative = getBrainNativeDb(projectRoot);
-            // Ensure nexus.db is available for symbol lookup
-            await getNexusDb(projectRoot);
-            const nexusNative = getNexusNativeDb(projectRoot);
-            if (!brainNative || !nexusNative)
-                return result;
-            // T11545: plasticity weight lives in the sibling nexus_relation_weights
-            // table — join it onto nexus_relations before aggregating per source.
-            const topSymbols = typedAll(nexusNative.prepare(`
-          SELECT n.id, n.name, n.label
-          FROM nexus_nodes n
-          LEFT JOIN (
-            SELECT rel.source_id, SUM(w.weight) AS total_weight
-            FROM nexus_relations rel
-            JOIN nexus_relation_weights w ON w.relation_id = rel.id
-            GROUP BY rel.source_id
-          ) r ON n.id = r.source_id
-          WHERE n.name IS NOT NULL AND n.name != ''
-          AND n.kind NOT IN ('community', 'process', 'folder')
-          ORDER BY COALESCE(r.total_weight, 0) DESC, n.indexed_at DESC
-          LIMIT 200
-        `));
-            if (topSymbols.length === 0)
-                return result;
-            // Build FTS query: "symbol1" OR "symbol2" OR ... (escaped for FTS5)
-            // Collect all symbol names for matching
-            const symbolNames = new Set();
-            const symbolMap = new Map(); // Map name -> first node with that name
-            for (const sym of topSymbols) {
-                if (sym.name) {
-                    symbolNames.add(sym.name);
-                    if (!symbolMap.has(sym.name)) {
-                        symbolMap.set(sym.name, sym);
-                    }
-                }
-            }
-            if (symbolNames.size === 0)
-                return result;
-            // Build FTS query: quoted terms OR'd together
-            const ftsQuery = Array.from(symbolNames)
-                .map((name) => `"${name.replace(/"/g, '""')}"`)
-                .join(' OR ');
-            // T11578 (AC4): conduit runtime read path repointed to the prefixed
-            // consolidated tables — `conduit_messages` + the `conduit_messages_fts`
-            // FTS5 index over it.
-            const messages = typedAll(conduitDb.prepare(`
-          SELECT id, content, attachments
-          FROM conduit_messages
-          WHERE attachments != '[]'
-             OR rowid IN (SELECT rowid FROM conduit_messages_fts WHERE content MATCH ?)
-          LIMIT 10000
-        `), ftsQuery);
-            result.scanned = messages.length;
-            if (messages.length === 0)
-                return result;
-            const now = new Date().toISOString().replace('T', ' ').slice(0, 19);
-            let edgesCreated = 0;
-            // Seam 3 (T11627): the brain page-graph edge writes below bypass the brain
-            // writer-thread chokepoint with a direct `brainNative` handle (project-tier
-            // consolidated cleo.db). Hold the project `bulk` lease for the whole write
-            // batch so they serialize against other writers. `off` → pass-through.
-            // T12044 (E6-L12d): pin the lease to the exact project cleo.db path resolved
-            // from the projectRoot parameter so concurrent projects route to their own rows.
-            await withWriterLease('project', 'bulk', async () => {
-                // For each message, scan content and attachments for symbol mentions
-                for (const msg of messages) {
-                    const corpus = `${msg.content}`;
-                    for (const [symbolName, nexusNode] of symbolMap.entries()) {
-                        // Case-insensitive check: does the symbol name appear in the message?
-                        const corpusLower = corpus.toLowerCase();
-                        const nameLower = symbolName.toLowerCase();
-                        if (corpusLower.includes(nameLower)) {
-                            const messageNodeId = `conduit:${msg.id}`;
-                            try {
-                                // Upsert a stub node for the message in brain_page_nodes (idempotent)
-                                brainNative
-                                    .prepare(`
-                  INSERT OR IGNORE INTO brain_page_nodes
-                    (id, node_type, label, quality_score, content_hash, metadata_json, last_activity_at, created_at, updated_at)
-                  VALUES (?, ?, ?, ?, NULL, NULL, ?, ?, ?)
-                `)
-                                    .run(messageNodeId, 'observation', `Conduit message: ${msg.id}`, 0.5, now, now, now);
-                                // Write the conduit_mentions_symbol edge (idempotent via INSERT OR IGNORE)
-                                brainNative
-                                    .prepare(`
-                  INSERT OR IGNORE INTO brain_page_edges
-                    (from_id, to_id, edge_type, weight, provenance, created_at)
-                  VALUES (?, ?, ?, ?, ?, ?)
-                `)
-                                    .run(messageNodeId, nexusNode.id, 'conduit_mentions_symbol', 1.0, 'auto:conduit-fts', now);
-                                edgesCreated++;
-                            }
-                            catch (edgeErr) {
-                                console.warn('[graph-memory-bridge] conduit edge insert failed:', edgeErr);
-                            }
-                            // Only link once per message per symbol (continue to next symbol)
-                            break;
-                        }
-                    }
-                }
-            }, { dbPath: conduitDbPath });
-            result.linked = edgesCreated;
-        }
-        finally {
-            try {
-                if (conduitDb.isOpen) {
-                    conduitDb.close();
-                }
-            }
-            catch {
-                // Ignore close errors
-            }
-        }
-    }
-    catch (err) {
-        console.warn('[graph-memory-bridge] linkConduitMessagesToSymbols failed:', err);
-    }
-    return result;
-}
 //# sourceMappingURL=graph-memory-bridge.js.map

package/dist/memory/graph-memory-bridge.js.map

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package/dist/memory/graph-queries.d.ts

@@ -124,4 +124,3 @@ export declare function contextBrainNode(projectRoot: string, nodeId: string): P
  * ```
  */
 export declare function graphStats(projectRoot: string): Promise<GraphStats>;
-//# sourceMappingURL=graph-queries.d.ts.map

package/dist/memory/import-from-provider.d.ts

@@ -107,4 +107,3 @@ export declare function memoryContentHash(title: string, body: string): string;
  * @throws {Error} When the source directory does not exist
  */
 export declare function importMemoryFiles(opts: ImportMemoryFilesOptions): Promise<ImportMemoryResult>;
-//# sourceMappingURL=import-from-provider.d.ts.map

package/dist/memory/index.d.ts

@@ -575,4 +575,3 @@ export * from './patterns.js';
 export * from './public-api.js';
 export * from './quality-feedback.js';
 export * from './session-narrative.js';
-//# sourceMappingURL=index.d.ts.map

package/dist/memory/learnings.d.ts

@@ -135,4 +135,3 @@ export declare function learningStats(projectRoot: string): Promise<{
     highConfidence: number;
     lowConfidence: number;
 }>;
-//# sourceMappingURL=learnings.d.ts.map

package/dist/memory/lessons-import.d.ts

@@ -172,4 +172,3 @@ export declare function applyLessonImport(projectRoot: string, sourceDir: string
  * ```
  */
 export declare function defaultLessonImportReceiptPath(projectRoot: string, importedAt: string): string;
-//# sourceMappingURL=lessons-import.d.ts.map

package/dist/memory/lessons.d.ts

@@ -64,4 +64,3 @@ export declare function listLessons(projectRoot: string, options?: {
     limit?: number;
     onStoreError?: (scope: 'project' | 'global', error: Error) => void;
 }): Promise<LessonEntry[]>;
-//# sourceMappingURL=lessons.d.ts.map

package/dist/memory/llm-backend-resolver.d.ts

@@ -33,7 +33,7 @@
  * OWNER OVERRIDE 2026-04-15: Cold tier MUST use claude-sonnet-4-6, NOT Haiku.
  *
  * Research basis: `.cleo/agent-outputs/T750-research-local-llm.md`
- * Spec reference: `docs/specs/memory-architecture-spec.md` §7
+ * Spec reference: `docs/spec/memory-architecture.md` §7
  *
  * @task T730
  * @task T11757
@@ -96,4 +96,3 @@ export declare function resolveLlmBackend(tier: ExtractionTier): Promise<Resolve
  * Returns `null` on any failure — never throws.
  */
 export declare function isOllamaAvailable(): Promise<boolean>;
-//# sourceMappingURL=llm-backend-resolver.d.ts.map

package/dist/memory/llm-backend-resolver.js

@@ -33,7 +33,7 @@
  * OWNER OVERRIDE 2026-04-15: Cold tier MUST use claude-sonnet-4-6, NOT Haiku.
  *
  * Research basis: `.cleo/agent-outputs/T750-research-local-llm.md`
- * Spec reference: `docs/specs/memory-architecture-spec.md` §7
+ * Spec reference: `docs/spec/memory-architecture.md` §7
  *
  * @task T730
  * @task T11757

package/dist/memory/llm-extraction.d.ts

@@ -104,4 +104,3 @@ export interface ExtractionReport {
  * ```
  */
 export declare function extractFromTranscript(options: ExtractFromTranscriptOptions): Promise<ExtractionReport>;
-//# sourceMappingURL=llm-extraction.d.ts.map

package/dist/memory/manifest-builder.d.ts

@@ -95,4 +95,3 @@ export declare const DEFAULT_MANIFEST_ENTRY_TYPE = "implementation";
  * ```
  */
 export declare function buildManifestEntryFromShorthand(shorthand: ManifestShorthand, now?: Date): ExtendedManifestEntry;
-//# sourceMappingURL=manifest-builder.d.ts.map

package/dist/memory/manifest-filter.d.ts

@@ -18,4 +18,3 @@ import type { ExtendedManifestEntry, ResearchFilter } from './index.js';
  * @task T4787
  */
 export declare function filterManifestEntries(entries: ExtendedManifestEntry[], filter: ResearchFilter): ExtendedManifestEntry[];
-//# sourceMappingURL=manifest-filter.d.ts.map

package/dist/memory/manifest-identity.d.ts

@@ -33,9 +33,8 @@ export declare const MANIFEST_FILE_MAX_LENGTH = 1024;
 /** Longest accepted single path segment of a `file` reference (filesystem NAME_MAX). */
 export declare const MANIFEST_FILE_SEGMENT_MAX_BYTES = 255;
 /**
- * Whether `value` is acceptable as a manifest linked task id: the canonical
- * `T<digits>` shape, or a structured `T…` id CLEO mints and stores
- * (`isStorableTaskId`, at most 64 characters, no whitespace or separators).
+ * Whether `value` is acceptable as a manifest linked task id: the task grammar
+ * `T<digits>` (T14324: the structured `T-RECONCILE-FOLLOWUP-…` ids are re-keyed).
  * A JSON blob, a path, or an over-long value is never accepted.
  *
  * @param value - Candidate task id.
@@ -168,4 +167,3 @@ export declare function resolveContainedFile(root: string, file: unknown): Conta
  *   (a directory throws `EISDIR`).
  */
 export declare function readContainedFile(root: string, file: unknown): ContainedFileRead;
-//# sourceMappingURL=manifest-identity.d.ts.map

package/dist/memory/manifest-identity.js

@@ -21,7 +21,7 @@
  */
 import { closeSync, constants as fsConstants, fstatSync, openSync, readFileSync, realpathSync, statSync, } from 'node:fs';
 import { isAbsolute, join, relative, sep } from 'node:path';
-import { isStorableTaskId, isTaskId } from '@cleocode/contracts/task-id.js';
+import { isTaskId } from '@cleocode/contracts/task-id.js';
 /** Longest accepted manifest entry id. */
 export const MANIFEST_ENTRY_ID_MAX_LENGTH = 200;
 /**
@@ -44,24 +44,15 @@ const UNC_REFERENCE = /^[\\/]{2}/;
 /** Control characters, which no id or path reference may contain. */
 const CONTROL_CHARS = /[\x00-\x1f\x7f]/;
 /**
- * Structured task ids CLEO mints on purpose alongside the canonical `T<digits>`
- * (`T-RECONCILE-FOLLOWUP-v2026.5.63-6`, see `isStorableTaskId`): a `T`, then
- * letters, digits, `.`, `_` and `-` only.
- */
-const STRUCTURED_TASK_ID = /^T[A-Za-z0-9._-]+$/;
-/**
- * Whether `value` is acceptable as a manifest linked task id: the canonical
- * `T<digits>` shape, or a structured `T…` id CLEO mints and stores
- * (`isStorableTaskId`, at most 64 characters, no whitespace or separators).
+ * Whether `value` is acceptable as a manifest linked task id: the task grammar
+ * `T<digits>` (T14324: the structured `T-RECONCILE-FOLLOWUP-…` ids are re-keyed).
  * A JSON blob, a path, or an over-long value is never accepted.
  *
  * @param value - Candidate task id.
  * @returns `true` when the value can name a task.
  */
 export function isManifestTaskId(value) {
-    if (isTaskId(value))
-        return true;
-    return typeof value === 'string' && isStorableTaskId(value) && STRUCTURED_TASK_ID.test(value);
+    return isTaskId(value);
 }
 /**
  * Truncate a value for display in an issue so a huge input cannot flood output.

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

@@ -1 +1 @@
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package/dist/memory/manifest-ingestion.d.ts

@@ -54,4 +54,3 @@ export declare function ingestRcasdDirectories(projectRoot: string, db: NodeSQLi
  */
 export declare function ingestLooseAgentOutputs(projectRoot: string, db: NodeSQLiteDatabase): Promise<IngestionResult>;
 export {};
-//# sourceMappingURL=manifest-ingestion.d.ts.map

package/dist/memory/memory-bridge.d.ts

@@ -71,4 +71,3 @@ export declare function refreshMemoryBridge(projectRoot: string, scope?: string,
  * @task T139 @epic T134
  */
 export declare function generateContextAwareContent(projectRoot: string, scope: string, currentTaskId?: string): Promise<void>;
-//# sourceMappingURL=memory-bridge.d.ts.map

package/dist/memory/mental-model-injection.d.ts

@@ -49,4 +49,3 @@ export declare const VALIDATE_ON_LOAD_PREAMBLE: string;
  * ```
  */
 export declare function buildMentalModelInjection(agentName: string, observations: MentalModelObservation[]): string;
-//# sourceMappingURL=mental-model-injection.d.ts.map

package/dist/memory/mental-model-queue.d.ts

@@ -92,4 +92,3 @@ export declare function _resetMentalModelQueueForTests(): void;
  * @param params - Observation parameters to evaluate.
  */
 export declare function isMentalModelObservation(params: ObserveBrainParams): boolean;
-//# sourceMappingURL=mental-model-queue.d.ts.map

package/dist/memory/nexus-plasticity.d.ts

@@ -133,4 +133,3 @@ export declare function applyPlasticityDecay(): Promise<PlasticityDecayResult>;
  * @returns Deduplicated source/target pairs ready for strengthenNexusCoAccess.
  */
 export declare function extractNexusPairsFromRetrievalLog(projectRoot: string, lookbackDays?: number): Promise<NexusEdgePair[]>;
-//# sourceMappingURL=nexus-plasticity.d.ts.map

package/dist/memory/observation-type-decision.d.ts

@@ -93,4 +93,3 @@ export interface ObservationTypeChoice {
  * @returns The chosen type with its source and confidence.
  */
 export declare function chooseObservationType(text: string, title: string | undefined, opts?: ChooseObservationTypeOptions): Promise<ObservationTypeChoice>;
-//# sourceMappingURL=observation-type-decision.d.ts.map

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

@@ -173,4 +173,3 @@ export declare function runObserver(projectRoot: string, sessionId?: string, opt
  * @returns ReflectorResult with counts.
  */
 export declare function runReflector(projectRoot: string, sessionId?: string): Promise<ReflectorResult>;
-//# sourceMappingURL=observer-reflector.d.ts.map

package/dist/memory/patterns.d.ts

@@ -170,4 +170,3 @@ export declare function patternStats(projectRoot: string): Promise<{
         frequency: number;
     } | null;
 }>;
-//# sourceMappingURL=patterns.d.ts.map

package/dist/memory/pipeline-manifest-sqlite.d.ts

@@ -294,6 +294,7 @@ export declare function pipelineManifestUpdate(id: string, patch: ManifestEntryP
 /**
  * Read unarchived entries from both manifest histories with physical provenance.
  * @param projectRoot - Explicit project root; takes priority over ambient project pins.
+ * @param entryId - Optional exact id, avoiding an unrelated full-history read.
  * @returns Entries retaining the existing fields and observed source tables/database path.
  * @throws EngineResultError when the same identity has conflicting persisted payloads.
  * @throws Error when storage reads fail; failure is never represented as an empty history.
@@ -305,7 +306,7 @@ export declare function pipelineManifestUpdate(id: string, patch: ManifestEntryP
  * const sources = entries.map((entry) => entry.provenance.tables);
  * ```
  */
-export declare function readManifestEntries(projectRoot?: string): Promise<Array<ManifestWithProvenance<ExtendedManifestEntry>>>;
+export declare function readManifestEntries(projectRoot?: string, entryId?: string): Promise<Array<ManifestWithProvenance<ExtendedManifestEntry>>>;
 /**
  * Filter manifest entries by criteria (alias for backward compatibility).
  */
@@ -332,4 +333,3 @@ export declare function migrateManifestJsonlToSqlite(projectRoot?: string): Prom
         issues: ManifestIdentityIssue[];
     }>;
 }>;
-//# sourceMappingURL=pipeline-manifest-sqlite.d.ts.map

package/dist/memory/pipeline-manifest-sqlite.js

@@ -1473,6 +1473,7 @@ export async function pipelineManifestUpdate(id, patch, projectRoot, options = {
 /**
  * Read unarchived entries from both manifest histories with physical provenance.
  * @param projectRoot - Explicit project root; takes priority over ambient project pins.
+ * @param entryId - Optional exact id, avoiding an unrelated full-history read.
  * @returns Entries retaining the existing fields and observed source tables/database path.
  * @throws EngineResultError when the same identity has conflicting persisted payloads.
  * @throws Error when storage reads fail; failure is never represented as an empty history.
@@ -1484,8 +1485,8 @@ export async function pipelineManifestUpdate(id, patch, projectRoot, options = {
  * const sources = entries.map((entry) => entry.provenance.tables);
  * ```
  */
-export async function readManifestEntries(projectRoot) {
-    return (await readRows(projectRoot)).map(rowToEntry);
+export async function readManifestEntries(projectRoot, entryId) {
+    return (await readRows(projectRoot, false, entryId)).map(rowToEntry);
 }
 /**
  * Filter manifest entries by criteria (alias for backward compatibility).