@cleocode/core 2026.8.1 → 2026.8.3

package/dist/store/memory-sqlite.d.ts

@@ -41,9 +41,23 @@
  */
 import type { DatabaseSync } from 'node:sqlite';
 import type { NodeSQLiteDatabase } from 'drizzle-orm/node-sqlite';
+import { type ProjectStore } from './dual-scope-db.js';
+import { type DomainBinding } from './ports/domain-binding.js';
 import * as brainSchema from './schema/memory-schema.js';
 /** Schema version for newly created brain databases. Single source of truth. */
 export declare const BRAIN_SCHEMA_VERSION = "1.0.0";
+/**
+ * The brain domain's bound value: its Drizzle handle plus the per-database
+ * `sqlite-vec` availability flag.
+ *
+ * @task T12038 (E6-L14)
+ */
+export interface BrainDomainHandle {
+    /** Drizzle instance typed against the legacy brain schema. */
+    readonly drizzle: NodeSQLiteDatabase;
+    /** Whether the `sqlite-vec` extension loaded for THIS database. */
+    readonly vecLoaded: boolean;
+}
 /**
  * Get the path to the brain-domain SQLite database file.
  *
@@ -66,9 +80,21 @@ export declare function getBrainDbPath(cwd?: string): string;
  */
 export declare function resolveBrainMigrationsFolder(): string;
 /**
- * Check whether the sqlite-vec extension is loaded for the current brain.db.
+ * Check whether the `sqlite-vec` extension is loaded for a project's brain
+ * database.
+ *
+ * ## E6-L14 (T12038) — now per-database
+ *
+ * This used to read a single process-wide boolean, so a project whose vec
+ * extension failed to load could report `true` because a DIFFERENT project
+ * had loaded it. The flag is now per-binding.
+ *
+ * Returns `false` when the brain domain is not bound for `cwd` yet — callers
+ * must `await getBrainDb(cwd)` / {@link bindBrainDomain} first.
+ *
+ * @param cwd - Project working directory. Defaults to the ambient project.
  */
-export declare function isBrainVecLoaded(): boolean;
+export declare function isBrainVecLoaded(cwd?: string): boolean;
 /**
  * Initialize the project-scope BRAIN domain SQLite database (lazy, singleton).
  *
@@ -96,6 +122,34 @@ export declare function isBrainVecLoaded(): boolean;
  * complete (migrations are async).
  */
 export declare function getBrainDb(cwd?: string): Promise<NodeSQLiteDatabase>;
+/**
+ * Bind the legacy brain schema to the {@link ProjectStore} for `cwd` and
+ * return the full binding (store + native handle + {@link BrainDomainHandle}).
+ *
+ * ## E6-L14 cutover (T12038)
+ *
+ * The ProjectStore-bound typed port that replaces this module's singleton
+ * quintet (`_db` / `_nativeDb` / `_dbPath` / `_initPromise` / `_vecLoaded`).
+ *
+ * The brain domain shares ONE `DatabaseSync` with the tasks domain (both are
+ * tables inside the same consolidated `cleo.db`). Under the old design that
+ * sharing was implicit and fragile: the tasks side could close the connection
+ * while the brain singleton still referenced it, and `observeBrain`'s
+ * cross-domain write-guard swallowed the resulting `database is not open` as
+ * "session absent" — silently nulling `sourceSessionId` (T12019/T12020).
+ * Binding both domains to the SAME store instance makes the sharing explicit:
+ * an eviction invalidates both bindings at once, by identity.
+ *
+ * Prefer this over {@link getBrainDb} when you also need the native handle,
+ * the per-database vec flag, or an explicit store for a cross-domain
+ * transaction with the tasks domain.
+ *
+ * @param cwd - Project working directory.
+ * @returns The live brain-domain binding.
+ *
+ * @task T12038 (E6-L14)
+ */
+export declare function bindBrainDomain(cwd?: string): Promise<DomainBinding<BrainDomainHandle, ProjectStore>>;
 /**
  * Close the brain-domain database connection and release resources.
  *
@@ -127,7 +181,7 @@ export declare function resetBrainDbState(): void;
  * Useful for direct PRAGMA calls or raw SQL operations.
  * Returns null if the database hasn't been initialized.
  */
-export declare function getBrainNativeDb(): DatabaseSync | null;
+export declare function getBrainNativeDb(cwd?: string): DatabaseSync | null;
 export type { NodeSQLiteDatabase };
 /**
  * Re-export brain schema for external use.

package/dist/store/memory-sqlite.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"memory-sqlite.d.ts","sourceRoot":"","sources":["../../src/store/memory-sqlite.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAwCG;AAKH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAKhD,OAAO,KAAK,EAAwB,kBAAkB,EAAE,MAAM,yBAAyB,CAAC;AAOxF,OAAO,EAAE,KAAK,YAAY,EAA0B,MAAM,oBAAoB,CAAC;AAU/E,OAAO,EAGL,KAAK,aAAa,EAGnB,MAAM,2BAA2B,CAAC;AAEnC,OAAO,KAAK,WAAW,MAAM,2BAA2B,CAAC;AA8BzD,gFAAgF;AAChF,eAAO,MAAM,oBAAoB,UAAU,CAAC;AAU5C;;;;;GAKG;AACH,MAAM,WAAW,iBAAiB;IAChC,8DAA8D;IAC9D,QAAQ,CAAC,OAAO,EAAE,kBAAkB,CAAC;IACrC,mEAAmE;IACnE,QAAQ,CAAC,SAAS,EAAE,OAAO,CAAC;CAC7B;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,cAAc,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,MAAM,CAEnD;AAED;;;;;;;GAOG;AACH,wBAAgB,4BAA4B,IAAI,MAAM,CAErD;AA6OD;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,gBAAgB,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,CAEtD;AA0BD;;;;;;;;;;;;;;;;;;;;;;;;;GAyBG;AACH,wBAAsB,UAAU,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,kBAAkB,CAAC,CAE1E;AAED;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;AACH,wBAAsB,eAAe,CACnC,GAAG,CAAC,EAAE,MAAM,GACX,OAAO,CAAC,aAAa,CAAC,iBAAiB,EAAE,YAAY,CAAC,CAAC,CAqDzD;AAED;;;;;;;;;;;;GAYG;AACH,wBAAgB,YAAY,IAAI,IAAI,CAInC;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,iBAAiB,IAAI,IAAI,CAExC;AAED;;;;GAIG;AACH,wBAAgB,gBAAgB,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,YAAY,GAAG,IAAI,CAElE;AAED,YAAY,EAAE,kBAAkB,EAAE,CAAC;AACnC;;GAEG;AACH,OAAO,EAAE,WAAW,EAAE,CAAC"}

package/dist/store/memory-sqlite.js

@@ -46,8 +46,11 @@ import { createRequire } from 'node:module';
 // native handle and re-wrap it with the legacy brain-schema drizzle instance so
 // existing callers (brainSchema.* queries) compile and run without change.
 import { getLogger } from '../logger.js';
-import { openDualScopeDb, resolveDualScopeDbPath } from './dual-scope-db.js';
+import { resolveDualScopeDbPath } from './dual-scope-db.js';
 import { createSafetyBackup, migrateWithRetry, reconcileBrainMigrationsForConsolidatedDb, reconcileJournal, tableExists, } from './migration-manager.js';
+// T12038: the brain domain no longer owns a singleton — the path-keyed binding
+// registry does. This module contributes only its schema reconciliation.
+import { bindProjectDomain, boundProjectNative, peekProjectDomain, releaseDomainBindings, } from './ports/domain-binding.js';
 import { resolveCorePackageMigrationsFolder } from './resolve-migrations-folder.js';
 import * as brainSchema from './schema/memory-schema.js';
 const _require = createRequire(import.meta.url);
@@ -77,14 +80,6 @@ function _getDrizzle() {
 }
 /** Schema version for newly created brain databases. Single source of truth. */
 export const BRAIN_SCHEMA_VERSION = '1.0.0';
-/** Singleton state for lazy initialization. */
-let _db = null;
-let _nativeDb = null;
-let _dbPath = null;
-/** Guard against concurrent initialization (async migration). */
-let _initPromise = null;
-/** Whether sqlite-vec extension loaded successfully. */
-let _vecLoaded = false;
 /**
  * Get the path to the brain-domain SQLite database file.
  *
@@ -207,7 +202,7 @@ function brainTablesAreConsolidatedShape(nativeDb) {
  * @internal
  * @task T11522
  */
-function establishLegacyBrainSchema(nativeDb, db) {
+function establishLegacyBrainSchema(nativeDb, db, dbPath) {
     const log = getLogger('brain-schema');
     if (brainTablesAreConsolidatedShape(nativeDb)) {
         // Drop the consolidated (exodus-target) brain tables so the legacy
@@ -268,8 +263,12 @@ function establishLegacyBrainSchema(nativeDb, db) {
     // pre-created, so run the full `drizzle-brain` migrate via the generic
     // reconcile (its Scenario-2 orphan-delete is safe here — a standalone brain.db
     // journal contains only brain hashes).
-    if (tableExists(nativeDb, 'brain_decisions') && _dbPath) {
-        createSafetyBackup(_dbPath);
+    // `dbPath` is passed explicitly (T12038) — it used to be read from the
+    // module-global `_dbPath`, which was still `null` on the first open because
+    // it was assigned AFTER this reconcile ran, so the safety backup never fired
+    // on the very path that needed it.
+    if (tableExists(nativeDb, 'brain_decisions')) {
+        createSafetyBackup(dbPath);
     }
     reconcileJournal(nativeDb, migrationsFolder, 'brain_decisions', 'brain');
     migrateWithRetry(db, migrationsFolder, nativeDb, 'brain_decisions', 'brain');
@@ -313,10 +312,22 @@ function initializeBrainVec(nativeDb) {
         .run();
 }
 /**
- * Check whether the sqlite-vec extension is loaded for the current brain.db.
+ * Check whether the `sqlite-vec` extension is loaded for a project's brain
+ * database.
+ *
+ * ## E6-L14 (T12038) — now per-database
+ *
+ * This used to read a single process-wide boolean, so a project whose vec
+ * extension failed to load could report `true` because a DIFFERENT project
+ * had loaded it. The flag is now per-binding.
+ *
+ * Returns `false` when the brain domain is not bound for `cwd` yet — callers
+ * must `await getBrainDb(cwd)` / {@link bindBrainDomain} first.
+ *
+ * @param cwd - Project working directory. Defaults to the ambient project.
  */
-export function isBrainVecLoaded() {
-    return _vecLoaded;
+export function isBrainVecLoaded(cwd) {
+    return peekProjectDomain('brain', cwd)?.db.vecLoaded ?? false;
 }
 /**
  * Initialize the default embedding provider when brain.embedding.enabled is true.
@@ -369,61 +380,47 @@ async function initEmbeddingProvider(cwd) {
  * complete (migrations are async).
  */
 export async function getBrainDb(cwd) {
-    const requestedPath = getBrainDbPath(cwd);
+    return (await bindBrainDomain(cwd)).db.drizzle;
+}
+/**
+ * Bind the legacy brain schema to the {@link ProjectStore} for `cwd` and
+ * return the full binding (store + native handle + {@link BrainDomainHandle}).
+ *
+ * ## E6-L14 cutover (T12038)
+ *
+ * The ProjectStore-bound typed port that replaces this module's singleton
+ * quintet (`_db` / `_nativeDb` / `_dbPath` / `_initPromise` / `_vecLoaded`).
+ *
+ * The brain domain shares ONE `DatabaseSync` with the tasks domain (both are
+ * tables inside the same consolidated `cleo.db`). Under the old design that
+ * sharing was implicit and fragile: the tasks side could close the connection
+ * while the brain singleton still referenced it, and `observeBrain`'s
+ * cross-domain write-guard swallowed the resulting `database is not open` as
+ * "session absent" — silently nulling `sourceSessionId` (T12019/T12020).
+ * Binding both domains to the SAME store instance makes the sharing explicit:
+ * an eviction invalidates both bindings at once, by identity.
+ *
+ * Prefer this over {@link getBrainDb} when you also need the native handle,
+ * the per-database vec flag, or an explicit store for a cross-domain
+ * transaction with the tasks domain.
+ *
+ * @param cwd - Project working directory.
+ * @returns The live brain-domain binding.
+ *
+ * @task T12038 (E6-L14)
+ */
+export async function bindBrainDomain(cwd) {
     // T1906: guard against prod-DB writes in test mode.
     const { assertTestEnv } = await import('./data-accessor.js');
-    assertTestEnv(requestedPath);
-    // If singleton exists but points to different path, reset it.
-    if (_db && _dbPath !== requestedPath) {
-        resetBrainDbState();
-    }
-    // Liveness guard (T11522): the brain domain shares the consolidated cleo.db
-    // handle with the tasks domain. The tasks side may have closed + re-opened the
-    // shared `DatabaseSync` (e.g. its `resetDbState()` / auto-recovery path) while
-    // our brain singleton still references the now-closed handle. Detect a stale
-    // (closed) handle and drop the singleton so we re-derive from the live
-    // openDualScopeDb cache below.
-    if (_db && (_nativeDb === null || !_nativeDb.isOpen)) {
-        resetBrainDbState();
-    }
-    if (_db)
-        return _db;
-    // If already initializing, wait for the in-flight init.
-    if (_initPromise)
-        return _initPromise;
-    _initPromise = (async () => {
-        // ── Dual-scope chokepoint delegation (T11522 · E6-L2) ─────────────────
-        // openDualScopeDb applies the pragma SSoT, creates the directory, runs the
-        // consolidated cleo-project migrations (which create the `brain_*` tables),
-        // and manages the singleton cache. We extract its native handle so we can
-        // re-wrap it with the legacy brain-schema for caller compatibility.
-        let nativeDb = null;
-        for (let attempt = 0; attempt < 2; attempt += 1) {
-            const dualHandle = await openDualScopeDb('project', cwd);
-            // Extract the underlying DatabaseSync. Drizzle exposes it via `$client`.
-            nativeDb = dualHandle.db.$client ?? null;
-            if (!nativeDb) {
-                throw new Error('E6-L2: openDualScopeDb returned a handle without $client — ' +
-                    'cannot extract DatabaseSync for legacy brain-schema wrapping.');
-            }
-            // A shared handle can be closed after the dual-scope cache checks it but
-            // before this await resumes. Re-open once; the cache then evicts the dead
-            // entry and returns the current live handle.
-            if (nativeDb.isOpen)
-                break;
-        }
-        if (!nativeDb?.isOpen) {
-            throw new Error('E6-L2: openDualScopeDb repeatedly returned a closed DatabaseSync handle.');
-        }
-        _nativeDb = nativeDb;
-        _dbPath = requestedPath;
+    assertTestEnv(getBrainDbPath(cwd));
+    return bindProjectDomain('brain', cwd, (nativeDb, store) => {
         // Load the sqlite-vec extension for vector similarity search (T5157). The
         // dual-scope handle is opened with `allowExtension: true`, so loading is
         // permitted. Non-fatal if unavailable — vec0 tables simply won't be created.
-        _vecLoaded = loadBrainVecExtension(nativeDb);
+        const vecLoaded = loadBrainVecExtension(nativeDb);
         // Wrap the native handle with the legacy brain-schema drizzle instance so
         // existing callers (brainSchema.* queries) continue to work unchanged.
-        const db = _getDrizzle()({ client: nativeDb });
+        const drizzle = _getDrizzle()({ client: nativeDb });
         // Reconcile the LEGACY brain-domain schema inside the consolidated cleo.db.
         // Since T11647 the consolidated `cleo.db` migration already creates every
         // `brain_*` table in the LEGACY RUNTIME shape (epoch-ms integer timestamps,
@@ -435,35 +432,27 @@ export async function getBrainDb(cwd) {
         // `drizzle-brain` migrate. The pre-T11647 DROP+recreate path is retained as
         // a defensive fallback for any DB still carrying the old consolidated shape.
         // (T11522 · T11647)
-        establishLegacyBrainSchema(nativeDb, db);
+        establishLegacyBrainSchema(nativeDb, drizzle, store.dbPath);
         // Create the vec0 virtual table for embeddings if the extension is loaded
         // (T5157). Must run after migrations so the schema is consistent.
-        if (_vecLoaded) {
+        if (vecLoaded) {
             initializeBrainVec(nativeDb);
         }
         // Seed schema version for new databases (no-op if already set).
         nativeDb
             .prepare(`INSERT OR IGNORE INTO brain_schema_meta (key, value) VALUES ('schemaVersion', '${BRAIN_SCHEMA_VERSION}')`)
             .run();
-        // Set singleton only after migrations complete.
-        _db = db;
         // Wire the default embedding provider when vec is loaded and embedding is
         // enabled. Best-effort, async, never blocks DB access. (T539)
-        if (_vecLoaded) {
+        if (vecLoaded) {
             setImmediate(() => {
                 initEmbeddingProvider(cwd).catch(() => {
                     // Non-fatal — embedding will be unavailable until next startup.
                 });
             });
         }
-        return db;
-    })();
-    try {
-        return await _initPromise;
-    }
-    finally {
-        _initPromise = null;
-    }
+        return { drizzle, vecLoaded };
+    });
 }
 /**
  * Close the brain-domain database connection and release resources.
@@ -479,13 +468,9 @@ export async function getBrainDb(cwd) {
  * coordinated reset (`closeAllDatabases` → `closeDb` → `_resetDualScopeDbCache`).
  */
 export function closeBrainDb() {
-    // Drop only the brain singleton references. Do NOT close `_nativeDb` — it is
+    // Drop only the brain-domain binding. Do NOT close the connection — it is
     // the shared dual-scope handle, possibly still in use by the tasks domain.
-    _nativeDb = null;
-    _db = null;
-    _dbPath = null;
-    _initPromise = null;
-    _vecLoaded = false;
+    releaseDomainBindings({ scope: 'project', domain: 'brain' });
 }
 /**
  * Reset brain-domain singleton state without saving.
@@ -499,19 +484,15 @@ export function closeBrainDb() {
  * shared with the tasks domain). Mirrors {@link closeBrainDb}.
  */
 export function resetBrainDbState() {
-    _nativeDb = null;
-    _db = null;
-    _dbPath = null;
-    _initPromise = null;
-    _vecLoaded = false;
+    releaseDomainBindings({ scope: 'project', domain: 'brain' });
 }
 /**
  * Get the underlying node:sqlite DatabaseSync instance for brain.db.
  * Useful for direct PRAGMA calls or raw SQL operations.
  * Returns null if the database hasn't been initialized.
  */
-export function getBrainNativeDb() {
-    return _nativeDb;
+export function getBrainNativeDb(cwd) {
+    return boundProjectNative('brain', cwd);
 }
 /**
  * Re-export brain schema for external use.

package/dist/store/memory-sqlite.js.map

@@ -1 +1 @@
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package/dist/store/nexus-sqlite.d.ts

@@ -69,9 +69,29 @@
  */
 import type { DatabaseSync } from 'node:sqlite';
 import type { NodeSQLiteDatabase } from 'drizzle-orm/node-sqlite';
+import { type ProjectStore } from './dual-scope-db.js';
+import { type DomainBinding } from './ports/domain-binding.js';
 import * as nexusSchema from './schema/nexus-schema.js';
 /** Schema version for newly created nexus databases. Single source of truth. */
 export declare const NEXUS_SCHEMA_VERSION = "1.0.0";
+/**
+ * The nexus domain's bound value: its Drizzle handle plus the GLOBAL registry
+ * path its ATTACH targets.
+ *
+ * The registry home (`getCleoHome()`) can change between calls. Carrying it in
+ * the binding lets {@link bindNexusDomain} detect the change and re-establish —
+ * which re-runs the GLOBAL consolidated migration before re-attaching, where a
+ * bare re-attach would bind an unmigrated file (→ "no such table:
+ * nexus_project_registry"). ADR-090 · T11648.
+ *
+ * @task T12039 (E6-L15)
+ */
+export interface NexusDomainHandle {
+    /** Drizzle instance typed against the nexus schema. */
+    readonly drizzle: NodeSQLiteDatabase;
+    /** Absolute path of the GLOBAL `cleo.db` currently ATTACHed. */
+    readonly registryPath: string;
+}
 /**
  * Returns the nexus GRAPH DB path — the consolidated PROJECT `cleo.db`
  * (`<projectRoot>/.cleo/cleo.db`), where the four code-graph tables
@@ -193,6 +213,28 @@ export declare function _resetNestedNexusWarningGate(): void;
  * @task T11648 (ADR-090 runtime read half — project-scope graph + global attach)
  */
 export declare function getNexusDb(): Promise<NodeSQLiteDatabase>;
+/**
+ * Bind the nexus schema to the {@link ProjectStore} holding the code graph,
+ * with the GLOBAL `cleo.db` ATTACHed for registry/identity reads.
+ *
+ * ## E6-L15 cutover (T12039)
+ *
+ * Replaces this module's singleton quintet (`_nexusDb` / `_nexusNativeDb` /
+ * `_nexusDbPath` / `_nexusRegistryPath` / `_nexusInitPromise`). Path keying,
+ * single-flight, and handle liveness move to the binding registry; this
+ * function keeps only what is genuinely nexus-specific — the two-scope open
+ * order and the registry ATTACH.
+ *
+ * The GLOBAL registry path is captured in the bound value rather than a
+ * separate module-global, so a `CLEO_HOME` change invalidates exactly this
+ * binding (and re-runs the global migration before re-attaching) instead of
+ * resetting a process-wide singleton that other projects also depended on.
+ *
+ * @returns The live nexus-domain binding.
+ *
+ * @task T12039 (E6-L15)
+ */
+export declare function bindNexusDomain(): Promise<DomainBinding<NexusDomainHandle, ProjectStore>>;
 /**
  * Close the nexus-domain database connection and release resources.
  *

package/dist/store/nexus-sqlite.d.ts.map

@@ -1 +1 @@
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