@cleocode/core 2026.4.45 → 2026.4.47

package/dist/index.js

@@ -11448,14 +11448,14 @@ function reconcileJournal(nativeDb, migrationsFolder, existenceTable, logSubsyst
       const dbHashes = new Set(dbEntries.map((e) => e.hash));
       const allLocalHashesPresentInDb = localMigrations.every((m) => dbHashes.has(m.hash));
       if (allLocalHashesPresentInDb) {
-        const log10 = getLogger(logSubsystem);
-        log10.debug(
+        const log11 = getLogger(logSubsystem);
+        log11.debug(
           { extra: orphanedEntries.length },
           `Migration journal has ${orphanedEntries.length} entries for migrations not known to this install (DB is ahead). Skipping reconciliation.`
         );
       } else {
-        const log10 = getLogger(logSubsystem);
-        log10.warn(
+        const log11 = getLogger(logSubsystem);
+        log11.warn(
           { orphaned: orphanedEntries.length },
           `Detected stale migration journal entries from a previous CLEO version. Reconciling.`
         );
@@ -11486,8 +11486,8 @@ function reconcileJournal(nativeDb, migrationsFolder, existenceTable, logSubsyst
         return cols.some((c) => c.name === column);
       });
       if (allColumnsExist) {
-        const log10 = getLogger(logSubsystem);
-        log10.warn(
+        const log11 = getLogger(logSubsystem);
+        log11.warn(
           { migration: migration.name, columns: alterMatches },
           `Detected partially-applied migration ${migration.name} \u2014 columns exist but journal entry missing. Auto-reconciling.`
         );
@@ -11505,8 +11505,8 @@ function reconcileJournal(nativeDb, migrationsFolder, existenceTable, logSubsyst
     for (const entry of unnamedEntries) {
       const migrationName = hashToName.get(entry.hash);
       if (!migrationName) continue;
-      const log10 = getLogger(logSubsystem);
-      log10.warn(
+      const log11 = getLogger(logSubsystem);
+      log11.warn(
         { id: entry.id, hash: entry.hash, name: migrationName },
         `Backfilling missing name on journal entry id=${entry.id} \u2014 Drizzle v1 beta requires name for applied-migration detection.`
       );
@@ -11550,8 +11550,8 @@ function ensureColumns(nativeDb, tableName, requiredColumns, logSubsystem) {
   const existingCols = new Set(columns.map((c) => c.name));
   for (const req of requiredColumns) {
     if (!existingCols.has(req.name)) {
-      const log10 = getLogger(logSubsystem);
-      log10.warn(
+      const log11 = getLogger(logSubsystem);
+      log11.warn(
         { column: req.name },
         `Adding missing column ${tableName}.${req.name} via ALTER TABLE`
       );
@@ -13511,7 +13511,7 @@ function getDbPath(cwd) {
   return join9(getCleoDirAbsolute(cwd), DB_FILENAME2);
 }
 async function autoRecoverFromBackup(nativeDb, dbPath, cwd) {
-  const log10 = getLogger("sqlite");
+  const log11 = getLogger("sqlite");
   try {
     const countResult = nativeDb.prepare("SELECT COUNT(*) as cnt FROM tasks").get();
     const taskCount = countResult?.cnt ?? 0;
@@ -13532,7 +13532,7 @@ async function autoRecoverFromBackup(nativeDb, dbPath, cwd) {
     if (backupTaskCount < MIN_BACKUP_TASK_COUNT) {
       return;
     }
-    log10.warn(
+    log11.warn(
       { dbPath, backupPath: newestBackup.path, backupTasks: backupTaskCount },
       `Empty database detected with ${backupTaskCount}-task backup available. Auto-recovering from backup. This likely happened because git-tracked WAL/SHM files were overwritten during a branch switch (T5188).`
     );
@@ -13550,7 +13550,7 @@ async function autoRecoverFromBackup(nativeDb, dbPath, cwd) {
     const tempPath = dbPath + ".recovery-tmp";
     copyFileSync4(newestBackup.path, tempPath);
     renameSync(tempPath, dbPath);
-    log10.info(
+    log11.info(
       { dbPath, backupPath: newestBackup.path, restoredTasks: backupTaskCount },
       "Database auto-recovered from backup successfully."
     );
@@ -13560,7 +13560,7 @@ async function autoRecoverFromBackup(nativeDb, dbPath, cwd) {
     runMigrations(restoredNativeDb, restoredDb);
     _db = restoredDb;
   } catch (err) {
-    log10.error({ err, dbPath }, "Auto-recovery from backup failed. Continuing with empty database.");
+    log11.error({ err, dbPath }, "Auto-recovery from backup failed. Continuing with empty database.");
   }
 }
 async function getDb(cwd) {
@@ -13594,7 +13594,7 @@ async function getDb(cwd) {
         const { execFileSync: execFileSync12 } = await import("node:child_process");
         const gitCwd = resolve3(dbPath, "..", "..");
         const filesToCheck = [dbPath, dbPath + "-wal", dbPath + "-shm"];
-        const log10 = getLogger("sqlite");
+        const log11 = getLogger("sqlite");
         for (const fileToCheck of filesToCheck) {
           try {
             execFileSync12("git", ["ls-files", "--error-unmatch", fileToCheck], {
@@ -13603,7 +13603,7 @@ async function getDb(cwd) {
             });
             const basename18 = fileToCheck.split(/[\\/]/).pop();
             const relPath = fileToCheck.replace(gitCwd + sep, "");
-            log10.warn(
+            log11.warn(
               { path: fileToCheck },
               `${basename18} is tracked by project git \u2014 this risks data loss on branch switch. Resolution (ADR-013 \xA79): \`git rm --cached ${relPath}\` and rely on \`.cleo/backups/sqlite/\` snapshots + \`cleo backup add\` for recovery.`
             );
@@ -14589,11 +14589,18 @@ var init_cross_db_cleanup = __esm({
 
 // packages/core/src/store/db-helpers.ts
 import { eq as eq4, inArray as inArray2 } from "drizzle-orm";
-async function upsertTask(db, row, archiveFields) {
+async function upsertTask(db, row, archiveFields, allowOrphanParent = false) {
   if (row.parentId) {
     const parent = await db.select({ id: tasks.id }).from(tasks).where(eq4(tasks.id, row.parentId)).limit(1).all();
     if (parent.length === 0) {
-      row = { ...row, parentId: null };
+      if (allowOrphanParent) {
+        row = { ...row, parentId: null };
+      } else {
+        log2.warn(
+          { taskId: row.id, parentId: row.parentId },
+          "upsertTask: parentId references a non-existent task \u2014 parent relationship may be lost"
+        );
+      }
     }
   }
   const values = archiveFields ? { ...row, ...archiveFields, status: "archived" } : row;
@@ -14737,10 +14744,13 @@ async function loadRelationsForTasks(db, tasks2) {
     }
   }
 }
+var log2;
 var init_db_helpers = __esm({
   "packages/core/src/store/db-helpers.ts"() {
     "use strict";
+    init_logger();
     init_tasks_schema();
+    log2 = getLogger("db-helpers");
   }
 });
 
@@ -15074,7 +15084,7 @@ async function createSqliteDataAccessor(cwd) {
             archiveReason: taskAny.archiveReason ?? "completed",
             cycleTimeDays: taskAny.cycleTimeDays ?? null
           };
-          await upsertTask(db, row, archiveFields);
+          await upsertTask(db, row, archiveFields, true);
           depBatch.push({ taskId: task.id, deps: task.depends ?? [] });
         }
         await batchUpdateDependencies(db, depBatch, validDepIds);
@@ -16061,7 +16071,7 @@ async function ensureSequenceValid(cwd, options) {
   if (!options?.validateSequence) return;
   const check2 = await checkSequence(cwd);
   if (!check2.valid) {
-    log2.warn({ counter: check2.counter, maxId: check2.maxIdInData }, "Sequence behind, repairing");
+    log3.warn({ counter: check2.counter, maxId: check2.maxIdInData }, "Sequence behind, repairing");
     const repair = await repairSequence(cwd);
     if (!repair.repaired && options.strict) {
       throw new DataSafetyError(`Sequence repair failed: ${repair.message}`, "SEQUENCE_INVALID", {
@@ -16078,7 +16088,7 @@ async function checkpoint(context, cwd, options) {
     stats.checkpoints++;
     stats.lastCheckpoint = /* @__PURE__ */ new Date();
   } catch (err) {
-    log2.warn({ err }, "Checkpoint failed (non-fatal)");
+    log3.warn({ err }, "Checkpoint failed (non-fatal)");
   }
   vacuumIntoBackup({ cwd }).catch(() => {
   });
@@ -16140,7 +16150,7 @@ async function safeAppendLog(accessor, entry, cwd, options) {
   stats.writes++;
   await checkpoint("log entry", cwd, opts);
 }
-var log2, DataSafetyError, DEFAULT_SAFETY, stats;
+var log3, DataSafetyError, DEFAULT_SAFETY, stats;
 var init_data_safety_central = __esm({
   "packages/core/src/store/data-safety-central.ts"() {
     "use strict";
@@ -16148,7 +16158,7 @@ var init_data_safety_central = __esm({
     init_sequence();
     init_git_checkpoint();
     init_sqlite_backup();
-    log2 = getLogger("data-safety");
+    log3 = getLogger("data-safety");
     DataSafetyError = class extends Error {
       constructor(message, code, context) {
         super(message);
@@ -16188,7 +16198,7 @@ function isSafetyDisabled() {
 }
 function wrapWithSafety(accessor, cwd) {
   if (isSafetyDisabled()) {
-    log3.warn(
+    log4.warn(
       "Safety disabled - emergency mode (CLEO_DISABLE_SAFETY=true). Data integrity checks bypassed."
     );
     return accessor;
@@ -16209,13 +16219,13 @@ function getSafetyStatus() {
     enabled: true
   };
 }
-var log3, SafetyDataAccessor;
+var log4, SafetyDataAccessor;
 var init_safety_data_accessor = __esm({
   "packages/core/src/store/safety-data-accessor.ts"() {
     "use strict";
     init_logger();
     init_data_safety_central();
-    log3 = getLogger("data-safety");
+    log4 = getLogger("data-safety");
     SafetyDataAccessor = class {
       /** The underlying accessor being wrapped. */
       inner;
@@ -16239,7 +16249,7 @@ var init_safety_data_accessor = __esm({
           ...config2
         };
         if (this.config.verbose) {
-          log3.debug({ engine: inner.engine }, "SafetyDataAccessor initialized");
+          log4.debug({ engine: inner.engine }, "SafetyDataAccessor initialized");
         }
       }
       /** The storage engine backing this accessor. */
@@ -16251,7 +16261,7 @@ var init_safety_data_accessor = __esm({
        */
       logVerbose(message) {
         if (this.config.verbose) {
-          log3.debug(message);
+          log4.debug(message);
         }
       }
       /**
@@ -20611,16 +20621,16 @@ async function queryAudit(options) {
       error: row.errorMessage ?? void 0
     }));
   } catch (err) {
-    log4.warn({ err }, "Failed to query audit entries from SQLite");
+    log5.warn({ err }, "Failed to query audit entries from SQLite");
     return [];
   }
 }
-var log4;
+var log5;
 var init_audit = __esm({
   "packages/core/src/audit.ts"() {
     "use strict";
     init_logger();
-    log4 = getLogger("audit");
+    log5 = getLogger("audit");
   }
 });
 
@@ -42965,13 +42975,16 @@ async function runTierPromotion(projectRoot) {
     try {
       shortToMedium = typedAll(
         nativeDb.prepare(`
-          SELECT id, citation_count, quality_score
+          SELECT id, citation_count, quality_score, verified
           FROM ${table}
           WHERE memory_tier = 'short'
             AND invalid_at IS NULL
             AND ${dateCol} < ?
-            AND verified = 1
-            AND (citation_count >= 3 OR quality_score >= 0.7)
+            AND (
+              citation_count >= 3
+              OR quality_score >= 0.7
+              OR verified = 1
+            )
         `),
         age24h
       );
@@ -42981,13 +42994,15 @@ async function runTierPromotion(projectRoot) {
     for (const row of shortToMedium) {
       try {
         nativeDb.prepare(`UPDATE ${table} SET memory_tier = 'medium', updated_at = ? WHERE id = ?`).run(now, row.id);
-        promoted.push({
-          id: row.id,
-          table,
-          fromTier: "short",
-          toTier: "medium",
-          reason: row.citation_count >= 3 ? `citationCount=${row.citation_count} >= 3, verified, age > 24h` : `qualityScore=${row.quality_score?.toFixed(2)} >= 0.70, verified, age > 24h`
-        });
+        let reason;
+        if (row.citation_count >= 3) {
+          reason = `citationCount=${row.citation_count} >= 3, age > 24h`;
+        } else if ((row.quality_score ?? 0) >= 0.7) {
+          reason = `qualityScore=${row.quality_score?.toFixed(2)} >= 0.70, age > 24h`;
+        } else {
+          reason = `verified=true, age > 24h`;
+        }
+        promoted.push({ id: row.id, table, fromTier: "short", toTier: "medium", reason });
       } catch {
       }
     }
@@ -42995,13 +43010,12 @@ async function runTierPromotion(projectRoot) {
     try {
       mediumToLong = typedAll(
         nativeDb.prepare(`
-          SELECT id, citation_count, quality_score
+          SELECT id, citation_count, quality_score, verified
           FROM ${table}
           WHERE memory_tier = 'medium'
             AND invalid_at IS NULL
             AND ${dateCol} < ?
-            AND verified = 1
-            AND citation_count >= 5
+            AND (citation_count >= 5 OR verified = 1)
         `),
         age7d
       );
@@ -43011,13 +43025,8 @@ async function runTierPromotion(projectRoot) {
     for (const row of mediumToLong) {
       try {
         nativeDb.prepare(`UPDATE ${table} SET memory_tier = 'long', updated_at = ? WHERE id = ?`).run(now, row.id);
-        promoted.push({
-          id: row.id,
-          table,
-          fromTier: "medium",
-          toTier: "long",
-          reason: `citationCount=${row.citation_count} >= 5, verified, age > 7d`
-        });
+        const reason = row.citation_count >= 5 ? `citationCount=${row.citation_count} >= 5, age > 7d` : `verified=true, age > 7d`;
+        promoted.push({ id: row.id, table, fromTier: "medium", toTier: "long", reason });
       } catch {
       }
     }
@@ -52550,9 +52559,7 @@ async function completeTask(options, cwd, accessor) {
     const parent = await acc.loadSingleTask(task.parentId);
     if (parent && parent.type === "epic" && !parent.noAutoComplete) {
       const siblings = await acc.getChildren(parent.id);
-      const allDone = siblings.every(
-        (c) => c.id === task.id || c.status === "done" || c.status === "cancelled"
-      );
+      const allDone = siblings.length > 0 && siblings.every((c) => c.id === task.id || c.status === "done" || c.status === "cancelled");
       if (allDone) {
         parent.status = "done";
         parent.completedAt = now;
@@ -59571,7 +59578,7 @@ init_logger();
 init_paths();
 init_tasks_schema();
 import { basename as basename6, relative as relative2 } from "node:path";
-var log5 = getLogger("lifecycle:evidence");
+var log6 = getLogger("lifecycle:evidence");
 async function recordEvidence(epicId, stage, uri, type, options) {
   const now = (/* @__PURE__ */ new Date()).toISOString();
   const stageId = `stage-${epicId}-${stage}`;
@@ -59598,7 +59605,7 @@ async function recordEvidence(epicId, stage, uri, type, options) {
       description: options?.description ?? null
     }).run();
   } catch (err) {
-    log5.warn({ err }, "Failed to write evidence to SQLite");
+    log6.warn({ err }, "Failed to write evidence to SQLite");
   }
   return record2;
 }
@@ -65897,7 +65904,7 @@ init_sqlite2();
 init_tasks_schema();
 import { randomUUID as randomUUID5 } from "node:crypto";
 import { and as and8, eq as eq11, sql as sql11 } from "drizzle-orm";
-var log6 = getLogger("link-store");
+var log7 = getLogger("link-store");
 async function getLinksByProvider(providerId, cwd) {
   const db = await getDb(cwd);
   const rows = await db.select().from(externalTaskLinks).where(eq11(externalTaskLinks.providerId, providerId));
@@ -65952,7 +65959,7 @@ async function ensureExternalTaskLinksTable(cwd) {
       )
     );
   } catch (err) {
-    log6.warn({ err }, "Failed to ensure external_task_links table exists");
+    log7.warn({ err }, "Failed to ensure external_task_links table exists");
     throw err;
   }
 }
@@ -66026,7 +66033,7 @@ init_brain_accessor();
 init_brain_sqlite();
 init_data_accessor();
 init_registry3();
-var log7 = getLogger("nexus:transfer");
+var log8 = getLogger("nexus:transfer");
 async function previewTransfer(params) {
   return executeTransferInternal({ ...params, dryRun: true });
 }
@@ -66167,7 +66174,7 @@ async function executeTransferInternal(params) {
       }
     }
   } catch (err) {
-    log7.warn(
+    log8.warn(
       { err, linksCreated },
       "Failed to create external_task_links during transfer \u2014 tasks were transferred successfully but provenance links could not be written"
     );
@@ -66195,7 +66202,7 @@ async function executeTransferInternal(params) {
       })
     });
   } catch (err) {
-    log7.warn({ err }, "nexus transfer audit write failed");
+    log8.warn({ err }, "nexus transfer audit write failed");
   }
   if (mode === "move") {
     let archived = 0;
@@ -66208,7 +66215,7 @@ async function executeTransferInternal(params) {
           });
           archived++;
         } catch (err) {
-          log7.warn({ err, taskId: entry.sourceId }, "failed to archive source task after transfer");
+          log8.warn({ err, taskId: entry.sourceId }, "failed to archive source task after transfer");
         }
       }
     }
@@ -66246,7 +66253,7 @@ async function executeTransferInternal(params) {
         }
       }
     } catch (err) {
-      log7.warn({ err }, "brain observation transfer failed");
+      log8.warn({ err }, "brain observation transfer failed");
     }
     result.brainObservationsTransferred = brainTransferred;
     result.manifest.brainObservationsTransferred = brainTransferred;
@@ -66294,8 +66301,8 @@ async function loadProjectACL(projectPath) {
 async function logAclFailure(projectPath) {
   try {
     const { getLogger: getLogger2 } = await Promise.resolve().then(() => (init_logger(), logger_exports));
-    const log10 = getLogger2("nexus.acl");
-    log10.warn({ projectPath }, "Failed to load ACL configuration, defaulting to deny-all");
+    const log11 = getLogger2("nexus.acl");
+    log11.warn({ projectPath }, "Failed to load ACL configuration, defaulting to deny-all");
   } catch {
   }
 }
@@ -66450,9 +66457,9 @@ async function executeOperation(operation, taskId, projectPath, accessor, direct
 async function logRouteAudit(directive, projectName, taskId, operation, success2, error48) {
   try {
     const { getLogger: getLogger2 } = await Promise.resolve().then(() => (init_logger(), logger_exports));
-    const log10 = getLogger2("nexus.route");
+    const log11 = getLogger2("nexus.route");
     const level = success2 ? "info" : "warn";
-    log10[level](
+    log11[level](
       {
         directive: directive.verb,
         agentId: directive.agentId,
@@ -75028,7 +75035,7 @@ init_data_accessor();
 
 // packages/core/src/stats/workflow-telemetry.ts
 init_logger();
-var log8 = getLogger("workflow-telemetry");
+var log9 = getLogger("workflow-telemetry");
 async function queryTasks(cwd, since) {
   try {
     const { getDb: getDb3 } = await Promise.resolve().then(() => (init_sqlite2(), sqlite_exports));
@@ -75050,7 +75057,7 @@ async function queryTasks(cwd, since) {
     }).from(tasks2).where(conditions.length > 0 ? and10(...conditions) : void 0).all();
     return rows;
   } catch (err) {
-    log8.warn({ err }, "Failed to query tasks for workflow telemetry");
+    log9.warn({ err }, "Failed to query tasks for workflow telemetry");
     return [];
   }
 }
@@ -75084,7 +75091,7 @@ async function queryCompletionAuditRows(cwd, since) {
       return isComplete;
     });
   } catch (err) {
-    log8.warn({ err }, "Failed to query audit log for workflow telemetry");
+    log9.warn({ err }, "Failed to query audit log for workflow telemetry");
     return [];
   }
 }
@@ -76540,11 +76547,11 @@ import { join as join87 } from "node:path";
 import { Readable } from "node:stream";
 import { pipeline } from "node:stream/promises";
 import { createGzip } from "node:zlib";
-var log9 = getLogger("prune");
+var log10 = getLogger("prune");
 async function pruneAuditLog(cleoDir, config2) {
   try {
     if (!config2.auditRetentionDays || config2.auditRetentionDays <= 0) {
-      log9.debug("auditRetentionDays is 0 or unset; skipping audit prune");
+      log10.debug("auditRetentionDays is 0 or unset; skipping audit prune");
       return { rowsArchived: 0, rowsDeleted: 0 };
     }
     const cutoff = new Date(Date.now() - config2.auditRetentionDays * 864e5).toISOString();
@@ -76555,7 +76562,7 @@ async function pruneAuditLog(cleoDir, config2) {
     const db = await getDb3(projectRoot);
     const oldRows = await db.select().from(auditLog2).where(lt3(auditLog2.timestamp, cutoff));
     if (oldRows.length === 0) {
-      log9.debug("No audit_log rows older than cutoff; nothing to prune");
+      log10.debug("No audit_log rows older than cutoff; nothing to prune");
       return { rowsArchived: 0, rowsDeleted: 0 };
     }
     let archivePath;
@@ -76573,17 +76580,17 @@ async function pruneAuditLog(cleoDir, config2) {
         const inStream = Readable.from([jsonlContent]);
         await pipeline(inStream, gzip, outStream);
         rowsArchived = oldRows.length;
-        log9.info(
+        log10.info(
           { archivePath, rowsArchived },
           `Archived ${rowsArchived} audit rows to ${archivePath}`
         );
       } catch (archiveErr) {
-        log9.warn({ err: archiveErr }, "Failed to archive audit rows; continuing with deletion");
+        log10.warn({ err: archiveErr }, "Failed to archive audit rows; continuing with deletion");
         archivePath = void 0;
       }
     }
     await db.delete(auditLog2).where(lt3(auditLog2.timestamp, cutoff)).run();
-    log9.info(
+    log10.info(
       { rowsDeleted: oldRows.length, cutoff },
       `Pruned ${oldRows.length} audit_log rows older than ${cutoff}`
     );
@@ -76593,7 +76600,7 @@ async function pruneAuditLog(cleoDir, config2) {
       archivePath
     };
   } catch (err) {
-    log9.warn({ err }, "audit log pruning failed");
+    log10.warn({ err }, "audit log pruning failed");
     return { rowsArchived: 0, rowsDeleted: 0 };
   }
 }