@cleocode/core 2026.10.3 → 2026.10.5-rc.ci.672

package/dist/doctor/malformed-task-ids.js.map

@@ -1 +1 @@
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+{"version":3,"file":"malformed-task-ids.js","sourceRoot":"","sources":["../../src/doctor/malformed-task-ids.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAgCG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AAClE,OAAO,EAAE,GAAG,EAAE,MAAM,aAAa,CAAC;AAClC,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAE5D;;;;;;;;GAQG;AACH,MAAM,eAAe,GAAG;IACtB,SAAS;IACT,YAAY;IACZ,YAAY;IACZ,gBAAgB;IAChB,WAAW;IACX,cAAc;CACN,CAAC;AAwDX;;;;;;;;;;;;;;;;;;;;;;GAsBG;AACH,MAAM,CAAC,KAAK,UAAU,oBAAoB,CACxC,GAAW,EACX,OAA0B,EAAE;IAE5B,MAAM,EAAE,EAAE,EAAE,GAAG,MAAM,eAAe,CAAC,SAAS,EAAE,GAAG,CAAC,CAAC;IAErD,4EAA4E;IAC5E,uEAAuE;IACvE,4EAA4E;IAC5E,gEAAgE;IAChE,MAAM,UAAU,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,CAC9B,GAAG,CAAA;;;yDAGkD,CACtD,CAAkD,CAAC;IAEpD,MAAM,IAAI,GAAG,UAAU;SACpB,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;SAC7D,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,eAAqC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC;IAE5E,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,CACvB,GAAG,CAAA,iDAAiD,CACrD,CAKC,CAAC;IAEH,MAAM,IAAI,GAAuB,EAAE,CAAC;IACpC,KAAK,MAAM,GAAG,IAAI,GAAG,EAAE,CAAC;QACtB,IAAI,gBAAgB,CAAC,GAAG,CAAC,EAAE,CAAC;YAAE,SAAS;QACvC,MAAM,EAAE,GAAG,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QAE1B,MAAM,UAAU,GAAoB,EAAE,CAAC;QACvC,KAAK,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,IAAI,IAAI,EAAE,CAAC;YACrC,6DAA6D;YAC7D,IAAI,KAAK,KAAK,aAAa,IAAI,MAAM,KAAK,WAAW;gBAAE,SAAS;YAEhE,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,CACvB,GAAG,CAAA,6BAA6B,GAAG,CAAC,UAAU,CAAC,KAAK,CAAC;oBACzC,GAAG,CAAC,UAAU,CAAC,MAAM,CAAC,MAAM,EAAE,EAAE,CAC7C,CAAkC,CAAC;YAEpC,MAAM,KAAK,GAAG,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC;YAC7B,IAAI,KAAK,GAAG,CAAC;gBAAE,UAAU,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,CAAC,CAAC;QAC3D,CAAC;QAED,IAAI,CAAC,IAAI,CAAC;YACR,EAAE;YACF,KAAK,EAAE,GAAG,CAAC,KAAK,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC;YACnD,MAAM,EAAE,GAAG,CAAC,MAAM,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC;YACtD,IAAI,EAAE,GAAG,CAAC,IAAI,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC;YAChD,cAAc,EAAE,UAAU;iBACvB,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,KAAK,yBAAyB,CAAC;iBACpD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;YACnC,UAAU;SACX,CAAC,CAAC;IACL,CAAC;IAED,IAAI,OAAO,GAAG,KAAK,CAAC;IACpB,MAAM,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;IAE5D,IAAI,IAAI,CAAC,GAAG,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxD,0EAA0E;QAC1E,yEAAyE;QACzE,0DAA0D;QAC1D,MAAM,EAAE,CAAC,GAAG,CAAC,GAAG,CAAA,OAAO,CAAC,CAAC;QACzB,IAAI,CAAC;YACH,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;gBACvB,MAAM,EAAE,CAAC,GAAG,CAAC,GAAG,CAAA,sCAAsC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC;YAClE,CAAC;YACD,MAAM,EAAE,CAAC,GAAG,CAAC,GAAG,CAAA,QAAQ,CAAC,CAAC;YAC1B,OAAO,GAAG,IAAI,CAAC;QACjB,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,MAAM,EAAE,CAAC,GAAG,CAAC,GAAG,CAAA,UAAU,CAAC,CAAC;YAC5B,MAAM,GAAG,CAAC;QACZ,CAAC;IACH,CAAC;IAED,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC;AAC9D,CAAC"}

package/dist/doctor/migrations.d.ts

@@ -9,16 +9,28 @@
  * migration's name but a different hash, the #1719 condition). Rows no known
  * lineage explains are listed too.
  *
+ * A journal rebuilt from empty on a store that already held its schema (most
+ * likely by a vault restore before T13104, which emptied it) is named, with
+ * how many rows the migrator stamped applied without running their SQL.
+ *
  * The store is opened as a read-only snapshot; nothing is written.
  *
  * @module
  * @task T12796
+ * @task T13104
  */
 import { type DualScope } from '../store/dual-scope-db.js';
 /** Lineages the project store's journal runs (the consolidated one first). */
 export declare const PROJECT_LINEAGES: readonly string[];
 /** Lineages the global store's journal runs. */
 export declare const GLOBAL_LINEAGES: readonly string[];
+/** A journal rebuilt on a store that already held its schema (T13104). */
+export interface RebuiltJournalReport {
+    /** Rows recorded applied without their SQL having run on this file (`applied_at` NULL). */
+    readonly stamped: number;
+    /** What happened and what it means. */
+    readonly detail: string;
+}
 /** One lineage's standing in a journal. */
 export interface LineageMigrationReport {
     readonly lineage: string;
@@ -52,6 +64,12 @@ export interface ScopeMigrationReport {
     }>;
     /** Rows no installed lineage knows (a newer build, or a foreign lineage). */
     readonly unknown: JournalRowReport[];
+    /**
+     * Set when the journal opens with the consolidated baseline stamped applied
+     * (`applied_at` NULL) instead of run: the migrator rebuilt it from empty on a
+     * store that already held the schema. `null` otherwise.
+     */
+    readonly rebuilt: RebuiltJournalReport | null;
 }
 /** The report of every scope. */
 export interface MigrationsReport {

package/dist/doctor/migrations.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"migrations.d.ts","sourceRoot":"","sources":["../../src/doctor/migrations.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;GAoBG;AAMH,OAAO,EAAE,KAAK,SAAS,EAA0B,MAAM,2BAA2B,CAAC;AAOnF,8EAA8E;AAC9E,eAAO,MAAM,gBAAgB,EAAE,SAAS,MAAM,EAM7C,CAAC;AAEF,gDAAgD;AAChD,eAAO,MAAM,eAAe,EAAE,SAAS,MAAM,EAK5C,CAAC;AAQF,0EAA0E;AAC1E,MAAM,WAAW,oBAAoB;IACnC,2FAA2F;IAC3F,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;IACzB,uCAAuC;IACvC,QAAQ,CAAC,MAAM,EAAE,MAAM,CAAC;CACzB;AAED,2CAA2C;AAC3C,MAAM,WAAW,sBAAsB;IACrC,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;IACzB,+CAA+C;IAC/C,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC;IACvB,gDAAgD;IAChD,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;IACzB,oDAAoD;IACpD,QAAQ,CAAC,OAAO,EAAE,MAAM,EAAE,CAAC;CAC5B;AAED,+CAA+C;AAC/C,MAAM,WAAW,gBAAgB;IAC/B,QAAQ,CAAC,EAAE,EAAE,MAAM,CAAC;IACpB,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI,CAAC;IAC7B,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;CACvB;AAED,mCAAmC;AACnC,MAAM,WAAW,oBAAoB;IACnC,QAAQ,CAAC,KAAK,EAAE,SAAS,CAAC;IAC1B,QAAQ,CAAC,MAAM,EAAE,MAAM,CAAC;IACxB,QAAQ,CAAC,MAAM,EAAE,OAAO,CAAC;IACzB,sCAAsC;IACtC,QAAQ,CAAC,WAAW,EAAE,MAAM,CAAC;IAC7B,mCAAmC;IACnC,QAAQ,CAAC,IAAI,EAAE,gBAAgB,GAAG,IAAI,CAAC;IACvC,QAAQ,CAAC,QAAQ,EAAE,sBAAsB,EAAE,CAAC;IAC5C,0EAA0E;IAC1E,QAAQ,CAAC,KAAK,EAAE,KAAK,CAAC,gBAAgB,GAAG;QAAE,QAAQ,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IAChF,6EAA6E;IAC7E,QAAQ,CAAC,OAAO,EAAE,gBAAgB,EAAE,CAAC;IACrC;;;;OAIG;IACH,QAAQ,CAAC,OAAO,EAAE,oBAAoB,GAAG,IAAI,CAAC;CAC/C;AAED,iCAAiC;AACjC,MAAM,WAAW,gBAAgB;IAC/B,QAAQ,CAAC,MAAM,EAAE,oBAAoB,EAAE,CAAC;CACzC;AAqBD;;;;;;;;GAQG;AACH,wBAAgB,cAAc,CAC5B,KAAK,EAAE,SAAS,EAChB,MAAM,EAAE,MAAM,EACd,QAAQ,GAAE,SAAS,MAAM,EAAkC,EAC3D,QAAQ,GAAE,CAAC,OAAO,EAAE,MAAM,KAAK,MAA2C,GACzE,oBAAoB,CA+EtB;AAqCD;;;GAGG;AACH,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,MAAM,GAAG,gBAAgB,CAOvE"}

package/dist/doctor/migrations.js

@@ -9,10 +9,15 @@
  * migration's name but a different hash, the #1719 condition). Rows no known
  * lineage explains are listed too.
  *
+ * A journal rebuilt from empty on a store that already held its schema (most
+ * likely by a vault restore before T13104, which emptied it) is named, with
+ * how many rows the migrator stamped applied without running their SQL.
+ *
  * The store is opened as a read-only snapshot; nothing is written.
  *
  * @module
  * @task T12796
+ * @task T13104
  */
 import { createHash } from 'node:crypto';
 import { existsSync, readdirSync, readFileSync } from 'node:fs';
@@ -35,6 +40,11 @@ export const GLOBAL_LINEAGES = [
     'drizzle-skills',
     'drizzle-telemetry',
 ];
+/** Each scope's consolidated lineage: its first migration opens a journal built on an empty store. */
+const BASELINE_LINEAGE = {
+    project: 'drizzle-cleo-project',
+    global: 'drizzle-cleo-global',
+};
 /** The lineage's migration files, hashed as drizzle's readMigrationFiles hashes them. */
 function localMigrations(folder) {
     if (!existsSync(folder))
@@ -59,7 +69,16 @@ function localMigrations(folder) {
  * @param folderOf - Folder resolver (tests pass their own).
  */
 export function inspectJournal(scope, dbPath, lineages = CONSOLIDATED_JOURNAL_LINEAGES, folderOf = resolveCorePackageMigrationsFolder) {
-    const base = { scope, dbPath, journalRows: 0, head: null, lineages: [], drift: [], unknown: [] };
+    const base = {
+        scope,
+        dbPath,
+        journalRows: 0,
+        head: null,
+        lineages: [],
+        drift: [],
+        unknown: [],
+        rebuilt: null,
+    };
     if (!existsSync(dbPath))
         return { ...base, exists: false };
     const snap = openCleoDbSnapshot(dbPath, { readOnly: true });
@@ -70,7 +89,8 @@ export function inspectJournal(scope, dbPath, lineages = CONSOLIDATED_JOURNAL_LI
             .get() !== undefined;
         if (!hasJournal)
             return { ...base, exists: true };
-        const hasName = db.prepare('PRAGMA main.table_info("__drizzle_migrations")').all().some((c) => c.name === 'name');
+        const columns = new Set(db.prepare('PRAGMA main.table_info("__drizzle_migrations")').all().map((c) => c.name));
+        const hasName = columns.has('name');
         const rows = db
             .prepare(`SELECT id, ${hasName ? 'name' : 'NULL AS name'}, hash FROM main."__drizzle_migrations" ORDER BY id`)
             .all();
@@ -115,12 +135,44 @@ export function inspectJournal(scope, dbPath, lineages = CONSOLIDATED_JOURNAL_LI
             lineages: reports,
             drift,
             unknown: rows.filter((r) => !known.has(r.hash) && !drift.some((d) => d.id === r.id)),
+            rebuilt: columns.has('applied_at')
+                ? rebuiltJournal(db, rows[0], localMigrations(folderOf(BASELINE_LINEAGE[scope]))[0])
+                : null,
         };
     }
     finally {
         snap.close();
     }
 }
+/**
+ * Whether a journal was rebuilt from empty on a store that already held its
+ * schema. A store built by its migrations runs the consolidated baseline first
+ * and records when (`applied_at`); a journal whose first row is that baseline
+ * with no `applied_at` was stamped by the reconciler, which only happens when
+ * the journal was empty and the baseline's tables already existed.
+ */
+function rebuiltJournal(db, first, baseline) {
+    if (!first || !baseline || first.hash !== baseline.hash)
+        return null;
+    const row = db
+        .prepare('SELECT applied_at IS NULL AS s FROM main."__drizzle_migrations" WHERE id = ?')
+        .get(first.id);
+    if (row?.s !== 1)
+        return null;
+    const stamped = db
+        .prepare('SELECT count(*) AS n FROM main."__drizzle_migrations" WHERE applied_at IS NULL')
+        .get().n;
+    return {
+        stamped,
+        detail: `the journal was rebuilt on a store that already held its schema: ${stamped} migration(s) ` +
+            'are recorded applied without their SQL having run on this file. This is most likely a ' +
+            'vault restore or pull before T13104, which emptied the journal; a journal emptied any ' +
+            'other way leaves the same mark. A store restored that way got its schema whole with the ' +
+            'snapshot, so the stamps hold; the rebuild may also have re-run old migrations, which ' +
+            "can leave an extra index on a legacy table. Otherwise the stamped migrations' indexes, " +
+            'triggers and CHECK constraints were never verified here.',
+    };
+}
 /**
  * The migration journals of the project store (at `projectRoot`) and the
  * global store. Read-only.

package/dist/doctor/migrations.js.map

@@ -1 +1 @@
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package/dist/doctor/row-identity-refill.d.ts

@@ -0,0 +1,43 @@
+/**
+ * `cleo doctor row-identity --refill`: the explicit remedy for a store whose
+ * identity predates the current recipe and that the open refused to refill
+ * because it could not be proven unshared (T13231; spec `t12341-uid-scheme`
+ * §12.1).
+ *
+ * A dry run by default. It prints the share verdict, its evidence (the local
+ * link, vault and journal state, and what Cleo Nexus answered) and the rows
+ * the refill would clear. `--apply` refills only when the verdict, with the
+ * Nexus answer folded in, is `unshared`: a pre-refill `VACUUM INTO` snapshot,
+ * then the from-scratch refill, inside the capture bracket when `sync.capture`
+ * is on.
+ *
+ * Cleo Nexus is asked read-only, with this machine's device credential,
+ * whether it holds ANY checkpoint or journal segment of the project from any
+ * device. "Present" refuses: a uid in the cloud is never rewritten locally
+ * (the future remedy is the T12344 re-key with aliases). "Unreachable" is
+ * unknown, and unknown refuses.
+ *
+ * @module
+ * @task T13231
+ */
+import type { RowIdentityNexusAnswer, RowIdentityRefillReport } from '@cleocode/contracts';
+/** Asks Cleo Nexus for the project's history; defaults to `askNexusProjectHistory`. */
+export type NexusHistoryProbe = (projectRoot: string) => Promise<RowIdentityNexusAnswer[]>;
+/** Options of {@link rowIdentityRefill}. */
+export interface RowIdentityRefillOptions {
+    /** Refill when the verdict allows it; a dry run without it. */
+    readonly apply?: boolean;
+    /** The Nexus probe (tests inject a mock; never the real cloud in tests). */
+    readonly probe?: NexusHistoryProbe;
+}
+/**
+ * Plan, and with `apply` run, the explicit from-scratch identity refill of a
+ * project store (T13231).
+ *
+ * @param projectRoot - Project directory.
+ * @param options - `apply`, and the Nexus probe.
+ * @returns The verdict, its evidence, the plan and what was done.
+ * @task T13231
+ */
+export declare function rowIdentityRefill(projectRoot: string, options?: RowIdentityRefillOptions): Promise<RowIdentityRefillReport>;
+//# sourceMappingURL=row-identity-refill.d.ts.map

package/dist/doctor/row-identity-refill.d.ts.map

@@ -0,0 +1 @@
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package/dist/doctor/row-identity-refill.js

@@ -0,0 +1,186 @@
+/**
+ * `cleo doctor row-identity --refill`: the explicit remedy for a store whose
+ * identity predates the current recipe and that the open refused to refill
+ * because it could not be proven unshared (T13231; spec `t12341-uid-scheme`
+ * §12.1).
+ *
+ * A dry run by default. It prints the share verdict, its evidence (the local
+ * link, vault and journal state, and what Cleo Nexus answered) and the rows
+ * the refill would clear. `--apply` refills only when the verdict, with the
+ * Nexus answer folded in, is `unshared`: a pre-refill `VACUUM INTO` snapshot,
+ * then the from-scratch refill, inside the capture bracket when `sync.capture`
+ * is on.
+ *
+ * Cleo Nexus is asked read-only, with this machine's device credential,
+ * whether it holds ANY checkpoint or journal segment of the project from any
+ * device. "Present" refuses: a uid in the cloud is never rewritten locally
+ * (the future remedy is the T12344 re-key with aliases). "Unreachable" is
+ * unknown, and unknown refuses.
+ *
+ * @module
+ * @task T13231
+ */
+import { existsSync } from 'node:fs';
+import { getDualScopeNativeDb, openDualScopeDb, resolveDualScopeDbPath, } from '../store/dual-scope-db.js';
+import { openCleoDbSnapshot } from '../store/open-cleo-db.js';
+import { fullRefillPlan, ROW_IDENTITY_META_TABLE, ROW_IDENTITY_REFILL_SNAPSHOT_KEY, rowIdentityRecipeCurrent, rowIdentityShareState, shareStateOf, } from '../store/row-identity.js';
+import { ROW_UID_FILL_FLAG, rowUidFillEnabled } from '../store/row-identity-flag.js';
+import { hasTable } from '../store/sync/schema.js';
+const RE_KEY_REMEDY = 'the cloud holds this project: its uids are never rewritten locally. The remedy is the re-key with aliases (T12344), not a refill';
+/** Fold the Nexus answers into the local verdict. */
+function verdictWith(local, nexus) {
+    // A linked store's `nexus-linked-no-vault` signal is resolved only when
+    // every origin answered "none".
+    const allNone = nexus.length > 0 && nexus.every((a) => a.answer === 'none');
+    const signals = local.signals.filter((s) => !(allNone && s.code === 'nexus-linked-no-vault'));
+    for (const a of nexus) {
+        if (a.answer === 'present') {
+            signals.push({
+                code: 'nexus-checkpoint',
+                kind: 'shared',
+                detail: `${a.apiUrl} holds ${a.checkpoints} checkpoint(s) and journal head ${a.headSeq} for project ${a.remoteProjectId}`,
+            });
+        }
+        else if (a.answer === 'error') {
+            signals.push({
+                code: 'nexus-unreachable',
+                kind: 'unknown',
+                detail: `${a.apiUrl} could not be asked: ${a.error ?? 'no answer'}`,
+            });
+        }
+    }
+    return shareStateOf(signals);
+}
+/** What to do next, from the verdict. */
+function remedyOf(verdict, fillEnabled) {
+    const codes = new Set(verdict.signals.map((s) => s.code));
+    const out = [];
+    if (codes.has('nexus-checkpoint') || codes.has('vault-pushed'))
+        out.push(RE_KEY_REMEDY);
+    if (codes.has('nexus-unreachable')) {
+        out.push('Cleo Nexus must answer: check `cleo login nexus` and the network, then re-run');
+    }
+    if (codes.has('unreadable'))
+        out.push('repair or remove the unreadable file, then re-run');
+    if (verdict.state === 'shared' && out.length === 0) {
+        out.push('local sync state references these uids: they are kept. The remedy is the re-key with aliases (T12344)');
+    }
+    if (verdict.state === 'unshared' && !fillEnabled) {
+        out.push(`set ${ROW_UID_FILL_FLAG}=1 for --apply (row uids are off in this process)`);
+    }
+    return out;
+}
+/** The undo instruction for a refill snapshot. */
+function undoOf(projectRoot, snapshot) {
+    const db = resolveDualScopeDbPath('project', projectRoot);
+    return ('STOP EVERY cleo PROCESS FIRST (agents, daemons, open terminals): a running writer would ' +
+        'overwrite or corrupt the restored file. No `cleo restore` verb restores cleo.db from a named ' +
+        'snapshot yet (T13240), so the undo is a file copy: ' +
+        `cp '${snapshot}' '${db}' && rm -f '${db}-wal' '${db}-shm'`);
+}
+/** The snapshot the last full refill recorded, if any. */
+function lastRefillSnapshot(db) {
+    if (!hasTable(db, ROW_IDENTITY_META_TABLE))
+        return null;
+    const row = db
+        .prepare(`SELECT value FROM main.${ROW_IDENTITY_META_TABLE} WHERE key = ?`)
+        .get(ROW_IDENTITY_REFILL_SNAPSHOT_KEY);
+    return row?.value ?? null;
+}
+/** Read the store's local verdict, marker and plan, read-only. */
+function readLocal(dbPath) {
+    const snap = openCleoDbSnapshot(dbPath, { readOnly: true });
+    try {
+        return {
+            local: rowIdentityShareState(snap.db),
+            recipeCurrent: rowIdentityRecipeCurrent(snap.db),
+            planned: fullRefillPlan(snap.db),
+            priorSnapshot: lastRefillSnapshot(snap.db),
+        };
+    }
+    finally {
+        snap.close();
+    }
+}
+/**
+ * Plan, and with `apply` run, the explicit from-scratch identity refill of a
+ * project store (T13231).
+ *
+ * @param projectRoot - Project directory.
+ * @param options - `apply`, and the Nexus probe.
+ * @returns The verdict, its evidence, the plan and what was done.
+ * @task T13231
+ */
+export async function rowIdentityRefill(projectRoot, options = {}) {
+    const dbPath = resolveDualScopeDbPath('project', projectRoot);
+    const fillEnabled = rowUidFillEnabled();
+    const empty = shareStateOf([]);
+    if (!existsSync(dbPath)) {
+        return {
+            projectRoot,
+            recipeCurrent: true,
+            fillEnabled,
+            local: empty,
+            nexus: [],
+            verdict: empty,
+            planned: {},
+            action: 'none',
+            remedy: ['no project store yet'],
+            applied: false,
+            snapshot: null,
+            undo: null,
+        };
+    }
+    const { local, recipeCurrent, planned, priorSnapshot } = readLocal(dbPath);
+    const probe = options.probe ??
+        (async (root) => (await import('../cloud/nexus-project-history.js')).askNexusProjectHistory(root));
+    const nexus = await probe(projectRoot);
+    const verdict = verdictWith(local, nexus);
+    const due = !recipeCurrent && Object.keys(planned).length > 0;
+    const action = !due ? 'none' : verdict.state === 'unshared' ? 'refill' : 'refuse';
+    const base = {
+        projectRoot,
+        recipeCurrent,
+        fillEnabled,
+        local,
+        nexus,
+        verdict,
+        planned,
+        action,
+        remedy: due ? remedyOf(verdict, fillEnabled) : ['the identity follows the current recipe'],
+        applied: false,
+        snapshot: null,
+        undo: null,
+    };
+    if (options.apply !== true || action !== 'refill' || !fillEnabled)
+        return base;
+    const nexusCheckedNone = nexus.length > 0 && nexus.every((a) => a.answer === 'none');
+    const db = getDualScopeNativeDb(await openDualScopeDb('project', projectRoot));
+    const { prepareRowIdentityUnderCapture } = await import('../store/sync/identity-fill.js');
+    const { report } = prepareRowIdentityUnderCapture(db, 'project', {
+        share: { nexusCheckedNone },
+    });
+    const snapshot = lastRefillSnapshot(db);
+    // The open itself may have refilled (an unlinked unshared store): a new
+    // snapshot under a current marker proves it.
+    const refilled = report?.refill === 'cleared' ||
+        (rowIdentityRecipeCurrent(db) && snapshot !== null && snapshot !== priorSnapshot);
+    if (!refilled) {
+        // The open re-checks the verdict: something changed since the plan.
+        return {
+            ...base,
+            action: 'refuse',
+            remedy: [
+                `the refill did not run (${report ? report.refill : 'the fill failed'}); see the log and re-run the dry run`,
+            ],
+        };
+    }
+    return {
+        ...base,
+        applied: true,
+        remedy: [],
+        snapshot,
+        undo: snapshot ? undoOf(projectRoot, snapshot) : null,
+    };
+}
+//# sourceMappingURL=row-identity-refill.js.map

package/dist/doctor/row-identity-refill.js.map

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package/dist/doctor/superseded-store.d.ts.map

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package/dist/doctor/superseded-store.js

@@ -38,6 +38,9 @@
 import { existsSync, statSync } from 'node:fs';
 import { join } from 'node:path';
 import { DatabaseSync } from 'node:sqlite';
+import { resolveCleoDir } from '../paths.js';
+import { loadPriorRecoveries, priorRecoveries } from '../store/exodus/prior-recoveries.js';
+import { TASK_ID_COLLISIONS_SQL } from '../store/exodus/task-id-collision-sql.js';
 /**
  * Legacy store filenames paired with the live table that replaced their
  * contents. The bare table name is the pre-migration one; the prefixed name is
@@ -113,6 +116,42 @@ function countMissingById(livePath, supersededPath, bareTable, liveTable) {
         }
     }
 }
+/**
+ * Legacy tasks in `supersededPath` whose id a DIFFERENT live task holds and
+ * that no live task matches yet (T13172): present by key, absent in substance.
+ * `null` when the comparison could not run.
+ */
+function countShadowedTasks(livePath, supersededPath, cleoDir) {
+    let db = null;
+    try {
+        db = new DatabaseSync(livePath, { readOnly: true }); // db-open-allowed: read-only probe of a superseded, unowned file
+        db.exec(`ATTACH DATABASE '${supersededPath.replace(/'/g, "''")}' AS legacy`);
+        // A table without the columns that tell two tasks apart cannot show a
+        // collision; its id-based count stands alone.
+        const hasColumns = (schema, table) => {
+            const names = new Set((db?.prepare(`PRAGMA ${schema}.table_info("${table}")`).all() ?? []).map((c) => c.name));
+            return names.has('title') && names.has('created_at');
+        };
+        if (!hasColumns('legacy', 'tasks') || !hasColumns('main', 'tasks_tasks'))
+            return 0;
+        loadPriorRecoveries(db, priorRecoveries(cleoDir));
+        const row = db
+            .prepare(`SELECT COUNT(*) AS c FROM (${TASK_ID_COLLISIONS_SQL}) WHERE recoveredAs IS NULL`)
+            .get();
+        return row?.c ?? null;
+    }
+    catch {
+        return null;
+    }
+    finally {
+        try {
+            db?.close();
+        }
+        catch {
+            /* already closed or never opened */
+        }
+    }
+}
 /** The supported command that copies stranded rows into `cleo.db` (T12319). */
 export const SUPERSEDED_STORE_RECONCILE_COMMAND = 'cleo doctor superseded-store --reconcile';
 /**
@@ -136,6 +175,8 @@ export const SUPERSEDED_STORE_RECONCILE_COMMAND = 'cleo doctor superseded-store
  */
 export function scanSupersededStores(projectRoot) {
     const liveStorePath = join(projectRoot, '.cleo', LIVE_STORE_FILENAME);
+    // Where the reconcile writes its receipts (T13183): the resolved .cleo.
+    const cleoDir = resolveCleoDir(projectRoot);
     const liveStoreExists = existsSync(liveStorePath);
     if (!liveStoreExists) {
         // No dual-scope store means nothing has been superseded — a pre-migration
@@ -166,7 +207,11 @@ export function scanSupersededStores(projectRoot) {
         // is the one case where being wrong loses data.
         // T12319: a file whose every row is already in cleo.db (reconciled) is
         // equally dead — proven by key, never by a count comparison.
-        const missingInLive = stat.size === 0 ? 0 : countMissingById(liveStorePath, path, bareTable, liveTable);
+        const missingById = stat.size === 0 ? 0 : countMissingById(liveStorePath, path, bareTable, liveTable);
+        // T13172: a legacy task whose id a different live task holds is present by
+        // key and absent in substance, so it counts as missing.
+        const shadowed = file === 'tasks.db' && stat.size !== 0 ? countShadowedTasks(liveStorePath, path, cleoDir) : 0;
+        const missingInLive = missingById === null || shadowed === null ? null : missingById + shadowed;
         const safeToArchive = (rowsInLive ?? 0) > 0 && (rowsInSuperseded === 0 || missingInLive === 0);
         let reason;
         if (stat.size === 0 && safeToArchive) {
@@ -194,7 +239,11 @@ export function scanSupersededStores(projectRoot) {
             reason =
                 `predates ${LIVE_STORE_FILENAME} but still holds ${rowsInSuperseded ?? 'an unknown number of'} ` +
                     `rows in ${bareTable} (live ${liveTable}: ${rowsInLive ?? 'unreadable'}; ` +
-                    `${missingInLive ?? 'an unknown number of'} missing from it). NOT recommended for removal. ` +
+                    `${missingInLive ?? 'an unknown number of'} missing from it` +
+                    (shadowed !== null && shadowed > 0
+                        ? `, of which ${shadowed} task id(s) a different live task now holds; the reconcile recovers those under new ids`
+                        : '') +
+                    `). NOT recommended for removal: keep ${file} until the reconcile reports them present. ` +
                     `Preview the copy with \`${SUPERSEDED_STORE_RECONCILE_COMMAND} --dry-run\`, then run ` +
                     `\`${SUPERSEDED_STORE_RECONCILE_COMMAND}\` to copy the missing rows into ` +
                     `${LIVE_STORE_FILENAME} (additive, verified, legacy file left in place).`;

package/dist/doctor/superseded-store.js.map

@@ -1 +1 @@
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package/dist/doctor/sync-repair.d.ts

@@ -0,0 +1,39 @@
+/**
+ * `cleo doctor sync-journal`: the repair diff of every suspect table (journal spec
+ * §4.4; S3d, T12987).
+ *
+ * Read-only by default: it opens the project `cleo.db` as a snapshot and
+ * plans the repair of each `suspect:` table (the I, U and D ops it would
+ * emit, the rows it would baseline, held and unidentified rows), writing
+ * nothing. `--repair` opens the store like any command and runs
+ * {@link repairSuspectTables}: seal what is pending, emit the repair ops in a
+ * `repair` frame per table, seal them, verify, and clear each suspect key
+ * that verifies.
+ *
+ * @module
+ * @task T12987
+ */
+import { type HoldsReport } from '../store/sync/held.js';
+import { type RepairReport } from '../store/sync/repair.js';
+/** What `cleo doctor sync-journal` reports. */
+export interface SyncRepairResult {
+    readonly dbPath: string;
+    readonly storeExists: boolean;
+    readonly report: RepairReport;
+    /** Tables that stay suspect (a plan in a dry run; unverified after a repair). */
+    readonly suspect: readonly string[];
+    /** Local writes a sync rebase holds, with the long holds and their reason (§3.5 Rule 5). */
+    readonly holds: HoldsReport;
+}
+/**
+ * Plan (default) or run (`repair`) the repair diff of the project store's
+ * suspect tables.
+ *
+ * @param projectRoot - The project root.
+ * @param options - `repair: true` writes; otherwise read-only.
+ */
+export declare function runSyncRepair(projectRoot: string, options?: {
+    readonly repair?: boolean;
+    readonly nowMs?: number;
+}): Promise<SyncRepairResult>;
+//# sourceMappingURL=sync-repair.d.ts.map

package/dist/doctor/sync-repair.d.ts.map

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