@cleocode/core 2026.8.1 → 2026.8.3

package/dist/store/sqlite.js

@@ -29,9 +29,12 @@ import { getLogger } from '../logger.js';
 // openDualScopeDb manages the DatabaseSync lifecycle, pragmas, and migrations
 // for the consolidated cleo.db. We extract the native handle and re-wrap it
 // with the legacy tasks-schema drizzle instance for E6 caller compatibility.
-import { _resetDualScopeDbCache, openDualScopeDb, resolveDualScopeDbPath, } from './dual-scope-db.js';
+import { _resetDualScopeDbCache, resolveDualScopeDbPath, } from './dual-scope-db.js';
 import { withLock } from './lock.js';
 import { createSafetyBackup, ensureColumns, migrateWithRetry, reconcileJournal, tableExists, } from './migration-manager.js';
+// T12037: the tasks domain no longer owns a singleton — the path-keyed binding
+// registry does. This module contributes only `establishTasksSchema`.
+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 { assertDbPathIsNotWorktreeResident } from './worktree-isolation-guard.js';
@@ -74,12 +77,12 @@ function _getDrizzle() {
 /** Schema version for newly created databases. Single source of truth. */
 export const SQLITE_SCHEMA_VERSION = '2.0.0';
 const SCHEMA_VERSION = SQLITE_SCHEMA_VERSION;
-/** Singleton state for lazy initialization. */
-let _db = null;
-let _nativeDb = null;
-let _dbPath = null;
-/** Guard against concurrent initialization (async migration). */
-let _initPromise = null;
+// ── No singleton state (E6-L13 · T12037) ─────────────────────────────────────
+// This module used to own `_db` / `_nativeDb` / `_dbPath` / `_initPromise`.
+// All four are gone: caching, path keying, single-flight, and handle liveness
+// belong to the path-keyed binding registry in `ports/domain-binding.ts`,
+// layered on the CleoRuntime store registry (T12036). This module now owns
+// only the tasks domain's schema reconciliation.
 /**
  * Get the path to the SQLite database file that {@link getDb} opens.
  *
@@ -224,19 +227,33 @@ function countBackupTasks(backupDb) {
  * assert exactly one restore occurs under the shared first-open lock. Production
  * code MUST reach this solely via {@link getDb}.
  *
+ * ## E6-L13 (T12037) — restore signals, it does not re-point
+ *
+ * Before the ProjectStore cutover this function re-opened the restored file
+ * and re-pointed the module-global `_db` / `_nativeDb` singletons itself.
+ * With those singletons gone it now performs ONLY the file-level restore and
+ * returns `true`, and {@link bindTasksDomain} re-binds every project domain
+ * against the restored file. That is strictly safer: the brain/conduit
+ * bindings sharing the same `cleo.db` are invalidated too, where the old
+ * singleton re-point left them holding a closed handle.
+ *
  * @param nativeDb - The freshly-opened consolidated handle (its `tasks_tasks` is
  *   probed for emptiness; closed before the file is overwritten on the restore path).
  * @param dbPath - Absolute path to the consolidated project `cleo.db`.
  * @param cwd - Working directory used to resolve the `.cleo/backups/sqlite/` dir.
+ * @returns `true` when the DB file was replaced from a backup (callers MUST
+ *   re-bind); `false` when no recovery was needed or possible.
  * @internal
  * @task T5188
  * @task T11662
+ * @task T12037
  */
 export async function autoRecoverFromBackup(nativeDb, dbPath, cwd) {
     // Lazy import openNativeDatabase at runtime to avoid any static-import
     // binding on sqlite-native.ts at module-init time.
     const { openNativeDatabase } = await import('./sqlite-native.js');
     const log = getLogger('sqlite');
+    let restored = false;
     try {
         // Count tasks in current database.
         // T11578 · AC1: the runtime now reads the PREFIXED consolidated table, so the
@@ -245,12 +262,12 @@ export async function autoRecoverFromBackup(nativeDb, dbPath, cwd) {
         const countResult = nativeDb.prepare('SELECT COUNT(*) as cnt FROM tasks_tasks').get();
         const taskCount = countResult?.cnt ?? 0;
         if (taskCount > 0)
-            return; // Database has data, no recovery needed
+            return false; // Database has data, no recovery needed
         // Database is empty — check for backups
         const backups = listSqliteBackups(cwd);
         if (backups.length === 0) {
             // No backups available — this is a genuinely new database
-            return;
+            return false;
         }
         // Check the newest backup for task count
         const newestBackup = backups[0];
@@ -269,7 +286,7 @@ export async function autoRecoverFromBackup(nativeDb, dbPath, cwd) {
         }
         if (backupTaskCount < MIN_BACKUP_TASK_COUNT) {
             // Backup also has very few tasks — not a reliable recovery source
-            return;
+            return false;
         }
         // ── Destructive restore under the shared first-open lock (T11662) ─────────
         // Everything above is a cheap, side-effect-free probe; from here we mutate
@@ -320,17 +337,12 @@ export async function autoRecoverFromBackup(nativeDb, dbPath, cwd) {
             // Rename in place — on the same filesystem this is atomic
             renameSync(tempPath, dbPath);
             log.info({ dbPath, backupPath: newestBackup.path, restoredTasks: backupTaskCount }, 'Database auto-recovered from backup successfully.');
-            // Re-open the restored database — update the native singleton.
-            // The dual-scope cache is now stale (its nativeDb was closed above);
-            // reset it so the singleton is re-established on next getDb().
+            // The dual-scope cache is now stale — its `DatabaseSync` was closed
+            // above and the file underneath it has been replaced. Evict it so the
+            // caller's re-bind opens a fresh connection to the restored file and
+            // re-runs migrations through the normal chokepoint path (T12037).
             _resetDualScopeDbCache();
-            const restoredNativeDb = openNativeDatabase(dbPath);
-            _nativeDb = restoredNativeDb;
-            // Re-run migrations on restored DB to ensure schema is current
-            const restoredDb = _getDrizzle()({ client: restoredNativeDb });
-            runMigrations(restoredNativeDb, restoredDb);
-            // Update the singleton drizzle instance
-            _db = restoredDb;
+            restored = true;
         }, 
         // Allow a generous stale window + retries: an exodus migration holding this
         // lock can take a while on a large fleet (matches on-open.ts), so a blocked
@@ -341,6 +353,7 @@ export async function autoRecoverFromBackup(nativeDb, dbPath, cwd) {
         // Auto-recovery failure is non-fatal — log and continue with empty DB
         log.error({ err, dbPath }, 'Auto-recovery from backup failed. Continuing with empty database.');
     }
+    return restored;
 }
 /**
  * Open (or return cached) the drizzle tasks-schema handle for the project scope.
@@ -361,104 +374,101 @@ export async function autoRecoverFromBackup(nativeDb, dbPath, cwd) {
  * initialization to complete (migrations are async).
  */
 export async function getDb(cwd) {
+    return (await bindTasksDomain(cwd)).db;
+}
+/**
+ * Bind the legacy tasks-schema to the {@link ProjectStore} for `cwd` and
+ * return the full binding (store + native handle + typed Drizzle instance).
+ *
+ * ## E6-L13 cutover (T12037)
+ *
+ * This is the ProjectStore-bound typed port that replaces the module-global
+ * singleton quartet (`_db` / `_nativeDb` / `_dbPath` / `_initPromise`) this
+ * facade used to own. Caching, path keying, single-flight, and handle
+ * liveness are now owned by {@link bindProjectDomain}; this function owns
+ * only the tasks domain's schema reconciliation.
+ *
+ * Three defect classes disappear with the singleton:
+ *
+ * - **Last-project-wins** — `_dbPath` tracked ONE project, so alternating
+ *   between two projects reset and re-migrated on every switch. Bindings are
+ *   now keyed by canonical `cleo.db` path.
+ * - **Cross-domain staleness** (T12019 / T12020) — the tasks singleton could
+ *   hold a `DatabaseSync` the brain domain had already closed. A binding is
+ *   valid only while the store instance it was established against is still
+ *   the live one, so an eviction invalidates it by identity.
+ * - **Band-aid reacquisition** (T12035) — the bounded retry loop that papered
+ *   over the above is deleted; the runtime registry handles liveness.
+ *
+ * Prefer this over {@link getDb} when you also need the native handle or an
+ * explicit store for a cross-domain transaction.
+ *
+ * @param cwd - Project working directory.
+ * @returns The live tasks-domain binding.
+ *
+ * @task T12037 (E6-L13)
+ */
+export async function bindTasksDomain(cwd) {
     // T9961 / T9806: worktree-isolation guard — defense-in-depth for direct
-    // getDb() callers that bypass openCleoDb('project', cwd).
-    // Fires before any DB file is touched, matching the openCleoDb chokepoint.
+    // callers that bypass openCleoDb('project', cwd). Fires before any DB file
+    // is touched, matching the openCleoDb chokepoint.
     assertDbPathIsNotWorktreeResident('tasks', cwd);
-    // Resolve the cleo.db path via the dual-scope helper (same logic as
-    // openDualScopeDb uses internally) to drive the singleton key.
-    const requestedPath = resolveDualScopeDbPath('project', cwd);
-    // If singleton exists but points to different path, reset it
-    if (_db && _dbPath !== requestedPath) {
-        resetDbState();
+    // `establish` runs ONLY on a cold bind (first open, or after an eviction).
+    // Capturing that here keeps auto-recovery a first-open concern: on a warm
+    // cache hit we must not re-probe `tasks_tasks` and re-scan the backup
+    // directory, which `getDb` does hundreds of times per process.
+    let coldBind = false;
+    const binding = await bindProjectDomain('tasks', cwd, (nativeDb, store) => {
+        coldBind = true;
+        return establishTasksSchema(nativeDb, store);
+    });
+    if (!coldBind)
+        return binding;
+    // ── T5188 auto-recovery (runs OUTSIDE establish) ──────────────────────────
+    // Recovery may REPLACE the `cleo.db` file, which invalidates every domain
+    // bound to it — not just this one. Running it here (rather than inside
+    // `establish`) lets us drop all project-domain bindings for the path and
+    // re-bind through the normal chokepoint, so brain/conduit never keep a
+    // handle to the pre-restore file. The re-bind cannot recurse: the restored
+    // DB is non-empty, so the emptiness probe short-circuits.
+    if (await autoRecoverFromBackup(binding.native, binding.store.dbPath, cwd)) {
+        releaseDomainBindings({ scope: 'project', dbPath: binding.store.dbPath });
+        return bindProjectDomain('tasks', cwd, establishTasksSchema);
     }
-    // Liveness guard (T12020): the tasks domain shares the consolidated project
-    // `cleo.db` `DatabaseSync` with the brain domain (both extract `$client` from
-    // the same `openDualScopeDb('project')` cache entry). A concurrent or deferred
-    // reset on the shared handle — e.g. another domain's `closeDb()` /
-    // `_resetDualScopeDbCache('project')`, or a fire-and-forget brain write firing
-    // across a test boundary — can close the underlying connection while THIS
-    // singleton still references it. Returning that stale (closed) handle makes
-    // the next query throw `database is not open`, which `observeBrain`'s cross-db
-    // session write-guard swallows and mistakes for "session absent" — silently
-    // nulling `sourceSessionId`. Detect the closed handle and re-derive from the
-    // live `openDualScopeDb` cache below. Mirrors the brain-domain guard in
-    // `getBrainDb` (memory-sqlite.ts, T11522).
-    if (_db && (_nativeDb === null || !_nativeDb.isOpen)) {
-        resetDbState();
-    }
-    if (_db)
-        return _db;
-    // If already initializing, wait for the in-flight init
-    if (_initPromise)
-        return _initPromise;
-    _initPromise = (async () => {
-        // ── Dual-scope chokepoint delegation (T11521 · E6-L1) ─────────────────
-        // openDualScopeDb applies pragma SSoT, creates the directory, runs cleo-project
-        // migrations, and manages the singleton cache. We extract its native handle
-        // so we can re-wrap it with the legacy tasks-schema for caller compatibility.
-        //
-        // T12035: bounded reacquisition loop — the shared consolidated DatabaseSync
-        // can be closed after openDualScopeDb checks the cache but before this await
-        // resumes (another domain's closeDb / reset / brain write firing across a
-        // microtask gap). Re-open once; the cache evicts the dead entry and returns
-        // the current live handle. This transitional guard will be removed by T12036's
-        // runtime ownership cutover.
-        let nativeDb = null;
-        for (let attempt = 0; attempt < 2; attempt += 1) {
-            const dualHandle = await openDualScopeDb('project', cwd);
-            nativeDb = dualHandle.db.$client ?? null;
-            if (!nativeDb) {
-                throw new Error('E6-L1: openDualScopeDb returned a handle without $client — ' +
-                    'cannot extract DatabaseSync for legacy tasks-schema wrapping.');
-            }
-            if (nativeDb.isOpen)
-                break;
-            // T12035: handle-liveness reacquisition — the shared consolidated
-            // DatabaseSync can be closed after openDualScopeDb checks the cache but
-            // before this await resumes (another domain's closeDb / reset / brain
-            // write firing across a microtask gap). Close this stale dual-scope
-            // handle — which evicts it from the singleton cache — so the next
-            // attempt opens a fresh, live connection. This transitional guard
-            // will be removed by T12036's runtime ownership cutover.
-            dualHandle.close();
-        }
-        if (!nativeDb?.isOpen) {
-            throw new Error('E6-L1: openDualScopeDb repeatedly returned a closed DatabaseSync handle.');
-        }
-        _nativeDb = nativeDb;
-        _dbPath = requestedPath;
-        // Wrap the native handle with the legacy tasks-schema drizzle instance.
-        // This allows all existing callers (using schema.tasks, schema.sessions, etc.)
-        // to continue querying the same DatabaseSync without change.
-        const db = _getDrizzle()({ client: nativeDb });
-        // Run legacy drizzle-tasks migrations against the shared cleo.db handle.
-        // During E3→E6 transition these create the old `tasks` table family alongside
-        // the new `tasks_tasks` tables from the consolidated schema migration.
-        runMigrations(nativeDb, db);
-        // Migration SQL contains PRAGMA foreign_keys=ON statements.
-        // In test environments, disable FKs after migration to allow test
-        // fixtures to insert data without full referential integrity.
-        if (process.env.VITEST) {
-            nativeDb.exec('PRAGMA foreign_keys=OFF');
-        }
-        // Seed schema version for new databases (no-op if already set)
-        nativeDb.exec(`INSERT OR IGNORE INTO schema_meta (key, value) VALUES ('schemaVersion', '${SCHEMA_VERSION}')`);
-        nativeDb.exec(`INSERT OR IGNORE INTO schema_meta (key, value) VALUES ('task_id_sequence', '{"counter":0,"lastId":"T000","checksum":"seed"}')`);
-        // Auto-recovery: detect empty database with available backups (T5188)
-        // Root cause: git-tracked WAL/SHM files get overwritten on branch switch,
-        // causing data loss when the WAL contained uncommitted writes.
-        await autoRecoverFromBackup(nativeDb, requestedPath, cwd);
-        // Set singleton only after migrations complete
-        _db = db;
-        return db;
-    })();
-    try {
-        return await _initPromise;
-    }
-    finally {
-        _initPromise = null;
+    return binding;
+}
+/**
+ * Reconcile the legacy tasks-domain schema against a consolidated `cleo.db`
+ * native handle and return the tasks-typed Drizzle instance.
+ *
+ * Idempotent by contract — {@link bindProjectDomain} re-runs it whenever the
+ * underlying store is evicted and re-opened.
+ *
+ * @param nativeDb - The shared consolidated connection.
+ * @param store - The {@link ProjectStore} that owns `nativeDb`.
+ * @returns The tasks-schema Drizzle handle.
+ *
+ * @task T12037 (E6-L13)
+ */
+function establishTasksSchema(nativeDb, store) {
+    // Wrap the shared native handle with the legacy tasks-schema drizzle
+    // instance so all existing callers (schema.tasks, schema.sessions, …)
+    // query the consolidated cleo.db unchanged.
+    const db = _getDrizzle()({ client: nativeDb });
+    // Run legacy drizzle-tasks migrations against the shared cleo.db handle.
+    // During the E3→E6 transition these create the old `tasks` table family
+    // alongside the consolidated `tasks_tasks` tables.
+    runMigrations(nativeDb, db, store.dbPath);
+    // 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');
     }
+    // Seed schema version for new databases (no-op if already set).
+    nativeDb.exec(`INSERT OR IGNORE INTO schema_meta (key, value) VALUES ('schemaVersion', '${SCHEMA_VERSION}')`);
+    nativeDb.exec(`INSERT OR IGNORE INTO schema_meta (key, value) VALUES ('task_id_sequence', '{"counter":0,"lastId":"T000","checksum":"seed"}')`);
+    return db;
 }
 /**
  * Resolve the absolute path to the drizzle-tasks migrations folder inside
@@ -513,11 +523,14 @@ const REQUIRED_SESSION_COLUMNS = [
  * @task T5185 - Retry+backoff for SQLITE_BUSY during migrations
  * @task T132 - Unified migration system
  */
-function runMigrations(nativeDb, db) {
+function runMigrations(nativeDb, db, dbPath) {
     const migrationsFolder = resolveMigrationsFolder();
-    // Safety backup before any migration work
-    if (tableExists(nativeDb, 'tasks') && _dbPath) {
-        createSafetyBackup(_dbPath);
+    // Safety backup before any migration work. `dbPath` is passed explicitly
+    // (T12037) — it used to be read from the module-global `_dbPath`, which was
+    // `null` on the auto-recovery re-migrate path and silently skipped the
+    // backup there.
+    if (tableExists(nativeDb, 'tasks')) {
+        createSafetyBackup(dbPath);
     }
     // Bootstrap baseline + reconcile stale journal entries.
     // T11829: the drizzle-tasks lineage runs against the SHARED consolidated cleo.db
@@ -566,30 +579,22 @@ function runMigrations(nativeDb, db) {
  * in `runMigrations → tableExists` for the very next `getDb()` caller.
  */
 export function closeDb() {
-    // Evict the PROJECT-scope dual-scope cache entries so the next openDualScopeDb()
-    // call opens a fresh DatabaseSync. Without this, the cache would return the
-    // stale handle whose nativeDb we're about to close below.
+    // Evict the PROJECT-scope dual-scope cache entries so the next bind opens a
+    // fresh DatabaseSync.
     //
     // E6-L4 (T11524): scope the eviction to `'project'`. The GLOBAL `cleo.db`
     // handle (nexus/signaldock/skills) now shares this same cache; an unscoped
     // reset here would close the global handle out from under an in-flight nexus
     // query (e.g. nexusSyncAll holding a handle while readProjectMeta opens + closes
     // a project accessor). Global teardown is the job of closeAllDatabases().
+    //
+    // E6-L13 (T12037): with the module-global singletons gone there is no
+    // private handle left to close here — the connection belongs to the
+    // dual-scope chokepoint, which `_resetDualScopeDbCache` closes. Dropping
+    // the project-domain bindings forces the next bind to re-establish the
+    // schema against whatever handle the chokepoint hands back.
     _resetDualScopeDbCache('project');
-    if (_nativeDb) {
-        try {
-            if (_nativeDb.isOpen) {
-                _nativeDb.close();
-            }
-        }
-        catch {
-            // Ignore close errors — _resetDualScopeDbCache already closed it
-        }
-        _nativeDb = null;
-    }
-    _db = null;
-    _dbPath = null;
-    _initPromise = null;
+    releaseDomainBindings({ scope: 'project' });
 }
 /**
  * Reset database singleton state without saving.
@@ -607,20 +612,7 @@ export function closeDb() {
  */
 export function resetDbState() {
     _resetDualScopeDbCache('project');
-    if (_nativeDb) {
-        try {
-            if (_nativeDb.isOpen) {
-                _nativeDb.close();
-            }
-        }
-        catch {
-            // Ignore close errors — _resetDualScopeDbCache already closed it
-        }
-        _nativeDb = null;
-    }
-    _db = null;
-    _dbPath = null;
-    _initPromise = null;
+    releaseDomainBindings({ scope: 'project' });
 }
 /**
  * Get the schema version from the database.
@@ -650,24 +642,38 @@ export function dbExists(cwd) {
     return existsSync(resolveDualScopeDbPath('project', cwd));
 }
 /**
- * Get the underlying node:sqlite DatabaseSync instance.
+ * Get the underlying `node:sqlite` `DatabaseSync` for the tasks domain.
  * Useful for direct PRAGMA calls or raw SQL operations.
- * Returns null if the database hasn't been initialized.
+ *
+ * ## E6-L13 (T12037) — now path-keyed
+ *
+ * This used to return a module-global that tracked whichever project was
+ * opened LAST. It now resolves the binding for `cwd`, so two projects live in
+ * one process without clobbering each other. Returns `null` when the tasks
+ * domain has not been bound for that project yet (or its connection has since
+ * closed) — callers must `await` {@link getDb} / {@link bindTasksDomain} first,
+ * which every existing call site already does.
+ *
+ * @param cwd - Project working directory. Defaults to the ambient project.
+ *
+ * @deprecated Read `.native` from {@link bindTasksDomain} instead — it cannot
+ *   return `null` and needs no prior await. Removed in T12040 (E6-L16).
  */
-export function getNativeDb() {
-    return _nativeDb;
+export function getNativeDb(cwd) {
+    return boundProjectNative('tasks', cwd);
 }
 /**
- * Get the underlying node:sqlite DatabaseSync instance for tasks.db.
+ * Get the underlying `node:sqlite` `DatabaseSync` for the tasks domain.
  *
- * ## E6-L1 façade (T11521)
+ * Thin alias of {@link getNativeDb} retained for call-site clarity in code
+ * that predates the consolidated `cleo.db`.
+ *
+ * @param cwd - Project working directory. Defaults to the ambient project.
  *
- * Thin facade delegating to {@link getNativeDb}. After the chokepoint
- * migration the native handle originates from {@link openDualScopeDb} —
- * callers receive the same `DatabaseSync` from `cleo.db`.
+ * @deprecated See {@link getNativeDb}.
  */
-export function getNativeTasksDb() {
-    return _nativeDb;
+export function getNativeTasksDb(cwd) {
+    return boundProjectNative('tasks', cwd);
 }
 /**
  * Re-export schema for external use.
@@ -701,5 +707,12 @@ export async function closeAllDatabases() {
     catch {
         /* module may not be loaded */
     }
+    // E6-L16 (T12040): the per-domain closers above drop bindings but each is
+    // scoped to its own domain (and `closeDb` only to the project scope). Full
+    // teardown means the runtime registry too — every project entry AND the
+    // global entry — otherwise a Windows temp-dir removal fails on a global
+    // `cleo.db` handle no domain closer owns. This is the ONLY caller that may
+    // tear down the whole runtime.
+    resetCleoRuntime();
 }
 //# sourceMappingURL=sqlite.js.map

package/dist/store/sqlite.js.map

@@ -1 +1 @@
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package/dist/store/tasks-sqlite.js

@@ -324,7 +324,7 @@ export async function getRelations(taskId, cwd) {
 /** Get the dependency chain (blockers) for a task using recursive CTE. */
 export async function getBlockerChain(taskId, cwd) {
     await getDb(cwd);
-    const nativeDb = getNativeDb();
+    const nativeDb = getNativeDb(cwd);
     if (!nativeDb)
         return [];
     const result = nativeDb
@@ -354,7 +354,7 @@ export async function getChildren(parentId, cwd) {
 /** Build a tree from a root task using recursive CTE. */
 export async function getSubtree(rootId, cwd) {
     await getDb(cwd);
-    const nativeDb = getNativeDb();
+    const nativeDb = getNativeDb(cwd);
     if (!nativeDb)
         return [];
     const rows = nativeDb

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

@@ -1 +1 @@
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package/dist/system/health.d.ts

@@ -66,10 +66,6 @@ export interface FixResult {
     action: 'fixed' | 'skipped' | 'failed';
     message: string;
 }
-/**
- * Run auto-fix for failed doctor checks by calling the corresponding ensure* functions.
- * Returns a list of fix results for each attempted repair.
- */
 export declare function runDoctorFixes(projectRoot: string): Promise<FixResult[]>;
 /**
  * Outcome of a startup health check. Tells the caller exactly what state

package/dist/system/health.d.ts.map

@@ -1 +1 @@
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