@cleocode/core 2026.9.20 → 2026.9.22

package/dist/store/sqlite.js

@@ -21,10 +21,12 @@
  * @task T4810 - Data loss prevention guards
  * @task T11521 - E6-L1: route getDb through openDualScopeDb (SG-DB-SUBSTRATE-V2)
  */
-import { copyFileSync, existsSync, renameSync, unlinkSync } from 'node:fs';
+import { copyFileSync, existsSync, realpathSync, renameSync, unlinkSync } from 'node:fs';
 import { createRequire } from 'node:module';
+import { basename, dirname, resolve } from 'node:path';
 import { eq } from 'drizzle-orm';
 import { getLogger } from '../logger.js';
+import { describeWorktreeOwner, isGitLinkedCheckout } from '../project-scope.js';
 // T11521: dual-scope chokepoint — all tasks.db opens now flow through here.
 // openDualScopeDb manages the DatabaseSync lifecycle, pragmas, and migrations
 // for the consolidated cleo.db. We extract the native handle and re-wrap it
@@ -38,6 +40,7 @@ import { createSafetyBackup, ensureColumns, isSqliteBusy, migrateWithRetry, reco
 import { bindProjectDomain, boundProjectNative, releaseDomainBindings, resetCleoRuntime, } from './ports/domain-binding.js';
 import { resolveConsolidatedJournalSiblings, resolveCorePackageMigrationsFolder, } from './resolve-migrations-folder.js';
 import { listSqliteBackups } from './sqlite-backup.js';
+import { collapseTwinTables, twinCollapseFailureOf } from './twin-collapse.js';
 import { assertDbPathIsNotWorktreeResident } from './worktree-isolation-guard.js';
 // node:sqlite access is isolated in the leaf module sqlite-native.ts to prevent
 // TDZ circular-import failures in the agent-resolver → dispatch-trace →
@@ -221,6 +224,46 @@ function countBackupTasks(backupDb) {
     }
     return 0;
 }
+/**
+ * Compare two directory paths by identity, following symlinks when both exist.
+ *
+ * @param a - First directory path.
+ * @param b - Second directory path.
+ * @returns `true` when both name the same directory.
+ * @task T12460
+ */
+function isSameDirectory(a, b) {
+    if (resolve(a) === resolve(b))
+        return true;
+    try {
+        return realpathSync(a) === realpathSync(b);
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Why auto-recovery must not restore into `dbPath`, or null when it may.
+ *
+ * A `<root>/.cleo/cleo.db` whose `<root>` is a linked git worktree is a
+ * diverged copy: restoring the parent's newest snapshot into it (~1.3 GB, and
+ * again into a `-pre-cleo.db.bak`) made every later write from the worktree
+ * land where nothing merges it back (T12460, field report T12677). The
+ * message names the project whose store the worktree must use.
+ *
+ * @param dbPath - Absolute path of the empty store auto-recovery would fill.
+ * @returns The refusal message, or null when `dbPath` is not worktree-resident.
+ * @task T12677
+ */
+export function worktreeRecoveryRefusal(dbPath) {
+    const storeCleoDir = dirname(dbPath);
+    const root = dirname(storeCleoDir);
+    if (basename(storeCleoDir) !== '.cleo' || !isGitLinkedCheckout(root))
+        return null;
+    return (`Auto-recovery refused: ${dbPath} lives inside the git worktree ${root}; ` +
+        `${describeWorktreeOwner(root)}. A worktree uses its owning project's store and ` +
+        'never receives a restored copy (T12460, T12677).');
+}
 /**
  * See the doc block above {@link countBackupTasks} for the full T5188/T11662
  * rationale. Exported (rather than module-private) ONLY so the T11662 concurrency
@@ -264,6 +307,15 @@ export async function autoRecoverFromBackup(nativeDb, dbPath, cwd) {
         const taskCount = countResult?.cnt ?? 0;
         if (taskCount > 0)
             return false; // Database has data, no recovery needed
+        // T12460: never restore INTO a worktree. A `<worktree>/.cleo/cleo.db` is a
+        // diverged copy; filling it with the parent's newest snapshot (~1.25 GB)
+        // made every later write there land in a store nothing merges back.
+        const storeCleoDir = dirname(dbPath);
+        const worktreeRefusal = worktreeRecoveryRefusal(dbPath);
+        if (worktreeRefusal !== null) {
+            log.warn({ dbPath }, worktreeRefusal);
+            return false;
+        }
         // Database is empty — check for backups
         const backups = listSqliteBackups(cwd);
         if (backups.length === 0) {
@@ -272,6 +324,14 @@ export async function autoRecoverFromBackup(nativeDb, dbPath, cwd) {
         }
         // Check the newest backup for task count
         const newestBackup = backups[0];
+        // T12460: a snapshot restores only the store it was taken of. The backup
+        // listing resolves its directory from `cwd` independently of `dbPath`;
+        // when the two disagree, restoring would copy ANOTHER store's data in.
+        const backupCleoDir = dirname(dirname(dirname(newestBackup.path)));
+        if (!isSameDirectory(backupCleoDir, storeCleoDir)) {
+            log.warn({ dbPath, backupPath: newestBackup.path }, 'Auto-recovery refused: the newest backup belongs to a different store (T12460).');
+            return false;
+        }
         // Open backup read-only to verify it has data.
         // Use openNativeDatabase (from sqlite-native.ts) — safe at runtime (no TDZ risk).
         const backupDb = openNativeDatabase(newestBackup.path, { readonly: true, enableWal: false });
@@ -460,13 +520,23 @@ function establishTasksSchema(nativeDb, store) {
     // During the E3→E6 transition these create the old `tasks` table family
     // alongside the consolidated `tasks_tasks` tables.
     runMigrations(nativeDb, db, store.dbPath);
+    // T12535: bring the prefixed twins up to date with their bare tables (the
+    // initial collapse snapshots first; later opens carry what an older build
+    // wrote since) before any caller reads them. A failure never fails the bind:
+    // reads are served from the merged TEMP shadows and the dispatch write guard
+    // refuses writes with E_TWIN_COLLAPSE_FAILED.
+    collapseTwinTables(nativeDb, store.dbPath, { onFailure: 'degrade' });
     // Migration SQL contains PRAGMA foreign_keys=ON statements. In test
     // environments, disable FKs after migration so fixtures can insert
     // without full referential integrity.
     if (process.env.VITEST) {
         nativeDb.exec('PRAGMA foreign_keys=OFF');
     }
-    seedTasksMeta(nativeDb);
+    // A store degraded by a failed twin collapse serves tasks_schema_meta from a
+    // read-only TEMP shadow that already holds the merged values; seeding it
+    // would abort (T12535).
+    if (twinCollapseFailureOf(nativeDb) === undefined)
+        seedTasksMeta(nativeDb);
     return db;
 }
 /**
@@ -476,14 +546,14 @@ function establishTasksSchema(nativeDb, store) {
  */
 export const TASK_ID_SEQUENCE_SEED = '{"counter":0,"lastId":"T000","checksum":"seed"}';
 /**
- * Seed the tasks domain's `schema_meta` defaults (no-op for keys already set).
+ * Seed the tasks domain's `tasks_schema_meta` defaults (no-op for keys already set).
  *
  * @param nativeDb - Connection on the project `cleo.db`.
  */
 export function seedTasksMeta(nativeDb) {
-    nativeDb.exec(`INSERT OR IGNORE INTO schema_meta (key, value) VALUES ('schemaVersion', '${SCHEMA_VERSION}')`);
+    nativeDb.exec(`INSERT OR IGNORE INTO tasks_schema_meta (key, value) VALUES ('schemaVersion', '${SCHEMA_VERSION}')`);
     nativeDb
-        .prepare("INSERT OR IGNORE INTO schema_meta (key, value) VALUES ('task_id_sequence', ?)")
+        .prepare("INSERT OR IGNORE INTO tasks_schema_meta (key, value) VALUES ('task_id_sequence', ?)")
         .run(TASK_ID_SEQUENCE_SEED);
 }
 /**

package/dist/store/sqlite.js.map

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package/dist/store/store-write-guard.d.ts

@@ -0,0 +1,28 @@
+/**
+ * Write guard for a project store whose twin collapse failed (T12535).
+ *
+ * When the collapse cannot run inside a domain bind, the bind still succeeds.
+ * Reads are served from TEMP shadows holding the merged, bare-authoritative
+ * view (see `twin-collapse.ts`), so nobody is locked out, but a write would
+ * land in a shadow or in a twin that is not in step. This module is the
+ * single question the write path asks: may this project's store be written?
+ * The CLI dispatch pipeline asks it for every mutating operation.
+ *
+ * @module
+ * @task T12535
+ */
+import type { CleoError } from '../errors.js';
+/**
+ * The `E_TWIN_COLLAPSE_FAILED` error that blocks writes to this project's
+ * store, or `null` when writes may proceed.
+ *
+ * Binds the tasks domain first (which runs the collapse), so the answer is
+ * current. A project without a store, or one whose bind fails for another
+ * reason, is not blocked here: the operation then fails, or not, on its own.
+ *
+ * @param projectRoot - Project directory.
+ * @returns The blocking error, or `null`.
+ * @task T12535
+ */
+export declare function storeWriteBlock(projectRoot: string): Promise<CleoError | null>;
+//# sourceMappingURL=store-write-guard.d.ts.map

package/dist/store/store-write-guard.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"store-write-guard.d.ts","sourceRoot":"","sources":["../../src/store/store-write-guard.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAGH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,cAAc,CAAC;AAK9C;;;;;;;;;;;GAWG;AACH,wBAAsB,eAAe,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,SAAS,GAAG,IAAI,CAAC,CAgBpF"}

package/dist/store/store-write-guard.js

@@ -0,0 +1,50 @@
+/**
+ * Write guard for a project store whose twin collapse failed (T12535).
+ *
+ * When the collapse cannot run inside a domain bind, the bind still succeeds.
+ * Reads are served from TEMP shadows holding the merged, bare-authoritative
+ * view (see `twin-collapse.ts`), so nobody is locked out, but a write would
+ * land in a shadow or in a twin that is not in step. This module is the
+ * single question the write path asks: may this project's store be written?
+ * The CLI dispatch pipeline asks it for every mutating operation.
+ *
+ * @module
+ * @task T12535
+ */
+import { existsSync } from 'node:fs';
+import { resolveDualScopeDbPath } from './dual-scope-db.js';
+import { getDb, getNativeDb } from './sqlite.js';
+import { twinCollapseError, twinCollapseFailureOf } from './twin-collapse.js';
+/**
+ * The `E_TWIN_COLLAPSE_FAILED` error that blocks writes to this project's
+ * store, or `null` when writes may proceed.
+ *
+ * Binds the tasks domain first (which runs the collapse), so the answer is
+ * current. A project without a store, or one whose bind fails for another
+ * reason, is not blocked here: the operation then fails, or not, on its own.
+ *
+ * @param projectRoot - Project directory.
+ * @returns The blocking error, or `null`.
+ * @task T12535
+ */
+export async function storeWriteBlock(projectRoot) {
+    let dbPath;
+    try {
+        dbPath = resolveDualScopeDbPath('project', projectRoot);
+    }
+    catch {
+        return null;
+    }
+    if (!existsSync(dbPath))
+        return null;
+    try {
+        await getDb(projectRoot);
+    }
+    catch {
+        return null;
+    }
+    const native = getNativeDb(projectRoot);
+    const failure = native ? twinCollapseFailureOf(native) : undefined;
+    return failure ? twinCollapseError(failure) : null;
+}
+//# sourceMappingURL=store-write-guard.js.map

package/dist/store/store-write-guard.js.map

@@ -0,0 +1 @@
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package/dist/store/table-classification.d.ts

@@ -0,0 +1,143 @@
+/**
+ * Table classification registry — the replication class of every physical
+ * table in the project and global `cleo.db` (Gate A).
+ *
+ * Every table a store can hold is either classified here (by an explicit
+ * entry or a pattern rule) or listed as pending an owner ruling. A table in
+ * neither place is UNCLASSIFIED, and the Gate A test
+ * (`__tests__/table-classification-gate.test.ts`) fails on it. That test
+ * enumerates `sqlite_master` of freshly migrated stores and of the committed
+ * live-store shape, so a table born in a migration, in runtime DDL, or in a
+ * legacy lineage cannot slip through.
+ *
+ * ## Keyed on physical names, not the Drizzle schema
+ *
+ * The runtime often writes the BARE legacy twin (`attachments`,
+ * `architecture_decisions`, `session_narrative`, …) rather than the prefixed
+ * table, while other bare twins are frozen copies nobody reads. A registry
+ * keyed on the Drizzle schema would classify the frozen copy and miss the
+ * live one, so both twins are listed here and the frozen ones carry
+ * `status: 'frozen-legacy'`, `liveTwin` and `dropTask` (T12535 collapses them).
+ *
+ * ## Two tiers: every table is backed up, portable tables also sync
+ *
+ * - **Tier 1, backup (the invariant).** Every table in both stores, with every
+ *   row, whatever its class (including `local-only`, `derived`, pending and
+ *   even unclassified tables), is backed up: encrypted client-side and
+ *   versioned per device, so any machine can be restored bit-for-bit. A class
+ *   NEVER exempts a table from backup. {@link TABLE_CLASS_POLICY} encodes this
+ *   as `backup: true` for every class, and the Gate A test asserts it.
+ * - **Tier 2, sync/merge across the owner's devices.** Only the portable
+ *   classes. `portable-personal` merges across the owner's own devices;
+ *   `portable-project` also merges into the project's shared space for
+ *   collaborators; `portable-secret` travels sealed end-to-end. `peer_scope`
+ *   governs sharing with OTHER people, never the owner's own machines.
+ *
+ * The test for a table: if this device died and the owner opened a new one,
+ * would an agent have to redo work or lose knowledge? If yes, it is portable.
+ *
+ * `derived` is deliberately NARROW: only what is rebuilt deterministically,
+ * cheaply and without an LLM. That is the FTS5/sqlite-vec shadow tables and
+ * the nexus code graph (rebuilt from source by `cleo nexus analyze`).
+ * Embeddings, sleep-cycle output and anything an LLM produced are NOT
+ * derived: regenerating them costs money or time. `local-only` is for state
+ * that is meaningless off-device: leases, queues, pids, paths, locations and
+ * fs-keyed caches.
+ *
+ * ## Follow-up: current learned weights (does not block Gate A)
+ *
+ * `brain_plasticity_events` and `brain_weight_history` are local-only for row
+ * sync (they are STDP event history, 14M+ inserts). A new device still needs
+ * the CURRENT learned weights. Deliver them either as a compacted
+ * "current weights" projection that syncs as `portable-personal`, or as a
+ * periodic compacted snapshot blob. Until then a new device restores them
+ * only from the tier-1 backup.
+ *
+ * ## Sources
+ *
+ * The classes come from the classification draft
+ * (`docs/research/table-classification-draft.md` in the cleo-nexus repo), the
+ * core owner's rulings in its §F, and the core owner's two-tier ruling of
+ * 2026-09-28 plus its follow-up ruling on the STDP tables. Table
+ * classification was delegated to agents by the owner, so these are cleo-dev
+ * rulings; the ruling supersedes earlier ones where they conflict (each such
+ * entry carries the old reasoning in its `note`). Rows marked
+ * `needs-owner-call` are provisional. Tables on the `pending` list have no
+ * class and never sync (they are still backed up), and the Gate A test fails
+ * while the list is non-empty: pending is a working state, never a merged
+ * one.
+ *
+ * @task T12332
+ * @epic T12322
+ * @module store/table-classification
+ */
+import type { TableClass, TableClassification, TableScope, TableScopeRegistry } from '@cleocode/contracts';
+/**
+ * The classification registry for the project `cleo.db`.
+ *
+ * @task T12332
+ */
+export declare const PROJECT_TABLE_REGISTRY: TableScopeRegistry;
+/**
+ * The classification registry for the global `cleo.db`.
+ *
+ * @task T12332
+ */
+export declare const GLOBAL_TABLE_REGISTRY: TableScopeRegistry;
+/**
+ * Every class a table can carry, in a stable order for reports.
+ *
+ * @task T12332
+ */
+export declare const TABLE_CLASSES: readonly TableClass[];
+/**
+ * What each class means for the two tiers.
+ *
+ * `backup` is `true` for EVERY class: that is the tier-1 invariant, and it is
+ * typed as the literal `true` so a class can never opt out. `sync` is tier 2.
+ *
+ * @task T12332
+ */
+export declare const TABLE_CLASS_POLICY: Readonly<Record<TableClass, {
+    backup: true;
+    sync: boolean;
+}>>;
+/**
+ * Return the registry for a scope.
+ *
+ * @param scope - Which `cleo.db` the table lives in.
+ * @returns That scope's registry.
+ * @task T12332
+ */
+export declare function getTableRegistry(scope: TableScope): TableScopeRegistry;
+/**
+ * Classify one physical table name.
+ *
+ * Lookup order: explicit entry, then pattern rule, then the pending list.
+ * Pure: no database is opened.
+ *
+ * @param scope - Which `cleo.db` the table lives in.
+ * @param name - The physical name as `sqlite_master` reports it.
+ * @returns The classification; `kind: 'unclassified'` fails Gate A.
+ *
+ * @example
+ * ```ts
+ * classifyTable('project', 'tasks_tasks'); // { kind: 'entry', class: 'portable-project', … }
+ * classifyTable('project', 'brain_observations_fts_idx'); // { kind: 'pattern', class: 'derived', … }
+ * ```
+ * @task T12332
+ */
+export declare function classifyTable(scope: TableScope, name: string): TableClassification;
+/**
+ * Whether a class syncs across devices (tier 2; sealed for secrets).
+ *
+ * A sync journal includes a table only when this is true for its class.
+ * Pending and unclassified tables have no class and never sync. Backup
+ * (tier 1) is not gated by this: every table is backed up.
+ *
+ * @param tableClass - The class to test.
+ * @returns `true` for the three portable classes.
+ * @task T12332
+ */
+export declare function isPortableTableClass(tableClass: TableClass): boolean;
+//# sourceMappingURL=table-classification.d.ts.map

package/dist/store/table-classification.d.ts.map

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