@cleocode/core 2026.9.16 → 2026.9.17

package/dist/nexus/projects-clean.d.ts

@@ -4,8 +4,15 @@
  * Purges project_registry rows matching configurable path/status criteria.
  * Supports dry-run mode and returns a summary result.
  *
+ * T12324: every run classifies the whole registry (missing path, temp path,
+ * test path), and an applied run removes the matched rows together with their
+ * `nexus_project_id_aliases` rows and a `nexus_audit_log` receipt in ONE
+ * transaction on the GLOBAL registry store — the store `--vacuum` compacts.
+ *
  * @task T1473
+ * @task T12324
  */
+import type { NexusProjectsCleanResult } from '@cleocode/contracts';
 import { type EngineResult } from '../engine-result.js';
 /** Thrown when no filter criteria are provided to cleanProjects. */
 export declare class NoCriteriaError extends Error {
@@ -25,9 +32,9 @@ export interface CleanProjectsOptions {
     dryRun: boolean;
     /** JS regex pattern matched against project_path. */
     pattern?: string;
-    /** Match paths containing a .temp/ segment. */
+    /** Match paths containing a .temp/ segment or under the OS temp directory (T12324). */
     includeTemp?: boolean;
-    /** Match paths containing tmp/test/fixture/scratch/sandbox segments. */
+    /** Match paths containing tmp/test(s)/__tests__/fixture(s)/scratch/sandbox segments. */
     includeTests?: boolean;
     /** Match rows where health_status is 'unhealthy'. */
     matchUnhealthy?: boolean;
@@ -43,7 +50,7 @@ export interface CleanProjectsOptions {
     matchPolluted?: boolean;
     /** After DB delete, `rm -rf` each matched path that still exists on disk (T9117). */
     removeFs?: boolean;
-    /** After DB delete, run sqlite VACUUM on nexus.db to reclaim space (T9117). */
+    /** After delete, VACUUM the GLOBAL registry store to reclaim space (T9117 · T12324). */
     vacuum?: boolean;
     /**
      * When matchPolluted is set and dryRun is false, write an audit JSONL to
@@ -51,37 +58,23 @@ export interface CleanProjectsOptions {
      */
     auditLog?: boolean;
 }
-/** Result envelope for {@link cleanProjects}. */
-export interface CleanProjectsResult {
-    /** Whether this was a dry-run (no deletions performed). */
-    dryRun: boolean;
-    /** Number of rows matching criteria. */
-    matched: number;
-    /** Number of rows actually deleted (0 when dryRun is true). */
-    purged: number;
-    /** Rows remaining after deletion. */
-    remaining: number;
-    /** Sample of matched project paths (first 10). */
-    sample: string[];
-    /** Total registry rows scanned. */
-    totalCount: number;
-    /** Number of on-disk paths successfully removed when `removeFs` is set (T9117). */
-    fsRemoved?: number;
-    /** Number of on-disk paths that failed to remove when `removeFs` is set (T9117). */
-    fsFailed?: number;
-    /** Bytes freed by VACUUM when `vacuum` is set (T9117). */
-    vacuumBytesFreed?: number;
-}
+/** Result envelope for {@link cleanProjects} (contract: `NexusProjectsCleanResult`). */
+export type CleanProjectsResult = NexusProjectsCleanResult;
 /**
  * Bulk-purge project registry rows matching configurable criteria.
  *
  * At least one of `pattern`, `includeTemp`, `includeTests`, `matchUnhealthy`,
- * or `matchNeverIndexed` must be set — otherwise throws {@link NoCriteriaError}.
- * If `pattern` is set but invalid, throws {@link InvalidPatternError}.
- * When `dryRun` is true, performs only a preview scan with no deletions.
+ * `matchNeverIndexed`, `matchOrphaned` or `matchPolluted` must be set —
+ * otherwise throws {@link NoCriteriaError}. If `pattern` is set but invalid,
+ * throws {@link InvalidPatternError}. When `dryRun` is true, performs only a
+ * preview scan with no deletions; the classification is reported either way.
+ *
+ * An applied run opens the GLOBAL registry store directly and, in one
+ * transaction, deletes the matched rows, every alias pointing at them, any
+ * pre-existing orphan alias, and writes the audit receipt.
  *
  * @param opts - Clean options.
- * @returns Clean result with match count and sample.
+ * @returns Clean result with match count, classification, and receipt.
  * @throws {NoCriteriaError} When no filter criteria are provided.
  * @throws {InvalidPatternError} When `opts.pattern` is not a valid regex.
  *

package/dist/nexus/projects-clean.d.ts.map

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package/dist/nexus/projects-clean.js

@@ -4,12 +4,22 @@
  * Purges project_registry rows matching configurable path/status criteria.
  * Supports dry-run mode and returns a summary result.
  *
+ * T12324: every run classifies the whole registry (missing path, temp path,
+ * test path), and an applied run removes the matched rows together with their
+ * `nexus_project_id_aliases` rows and a `nexus_audit_log` receipt in ONE
+ * transaction on the GLOBAL registry store — the store `--vacuum` compacts.
+ *
  * @task T1473
+ * @task T12324
  */
+import { randomUUID } from 'node:crypto';
 import { existsSync, statSync } from 'node:fs';
 import { rm } from 'node:fs/promises';
 import path from 'node:path';
+import { inArray, sql } from 'drizzle-orm';
 import { engineError, engineSuccess } from '../engine-result.js';
+import { getCleoHome } from '../paths.js';
+import { isEphemeralPath } from './registry-hygiene.js';
 /** Thrown when no filter criteria are provided to cleanProjects. */
 export class NoCriteriaError extends Error {
     /** @override */
@@ -28,23 +38,43 @@ export class InvalidPatternError extends Error {
     }
 }
 const TEMP_RE = /(^|\/)\.temp(\/|$)/;
-const TESTS_RE = /(^|\/)(tmp|test|fixture|scratch|sandbox)(\/|$)/;
+// T12324: `__tests__` and plural `tests`/`fixtures` are fixture homes too.
+const TESTS_RE = /(^|\/)(tmp|tests?|__tests__|fixtures?|scratch|sandbox)(\/|$)/;
 function portablePathForMatch(p) {
     return p.replace(/\\/g, '/');
 }
 function pathSegmentCount(p) {
     return portablePathForMatch(p).split('/').filter(Boolean).length;
 }
+/** Report whether a registry path is temp-like (`.temp/` segment or OS temp root). */
+function isTempPath(projectPath) {
+    return TEMP_RE.test(portablePathForMatch(projectPath)) || isEphemeralPath(projectPath);
+}
+/** Report whether a registry path carries a test-fixture segment. */
+function isTestPath(projectPath) {
+    return TESTS_RE.test(portablePathForMatch(projectPath));
+}
+/** Total bytes of the store's pages, read before and after VACUUM. */
+function storeBytes(db) {
+    const pages = db.get(sql `PRAGMA page_count`).page_count;
+    const size = db.get(sql `PRAGMA page_size`).page_size;
+    return pages * size;
+}
 /**
  * Bulk-purge project registry rows matching configurable criteria.
  *
  * At least one of `pattern`, `includeTemp`, `includeTests`, `matchUnhealthy`,
- * or `matchNeverIndexed` must be set — otherwise throws {@link NoCriteriaError}.
- * If `pattern` is set but invalid, throws {@link InvalidPatternError}.
- * When `dryRun` is true, performs only a preview scan with no deletions.
+ * `matchNeverIndexed`, `matchOrphaned` or `matchPolluted` must be set —
+ * otherwise throws {@link NoCriteriaError}. If `pattern` is set but invalid,
+ * throws {@link InvalidPatternError}. When `dryRun` is true, performs only a
+ * preview scan with no deletions; the classification is reported either way.
+ *
+ * An applied run opens the GLOBAL registry store directly and, in one
+ * transaction, deletes the matched rows, every alias pointing at them, any
+ * pre-existing orphan alias, and writes the audit receipt.
  *
  * @param opts - Clean options.
- * @returns Clean result with match count and sample.
+ * @returns Clean result with match count, classification, and receipt.
  * @throws {NoCriteriaError} When no filter criteria are provided.
  * @throws {InvalidPatternError} When `opts.pattern` is not a valid regex.
  *
@@ -72,38 +102,23 @@ export async function cleanProjects(opts) {
             throw new InvalidPatternError(opts.pattern, err);
         }
     }
-    /**
-     * Return true if a project matches any active criteria.
-     */
-    function matchesCriteria(projectPath, healthStatus, lastIndexed) {
-        const normalizedProjectPath = portablePathForMatch(projectPath);
-        if (patternRegex?.test(projectPath) || patternRegex?.test(normalizedProjectPath))
-            return true;
-        if (opts.includeTemp && TEMP_RE.test(normalizedProjectPath))
-            return true;
-        if (opts.includeTests && TESTS_RE.test(normalizedProjectPath))
-            return true;
-        if (opts.matchUnhealthy && healthStatus === 'unhealthy')
-            return true;
-        if (opts.matchNeverIndexed && lastIndexed === null)
-            return true;
-        if (opts.matchOrphaned && !existsSync(projectPath))
-            return true;
-        return false;
-    }
-    const { getNexusDb } = await import('../store/nexus-sqlite.js');
-    const { projectRegistry: regTable, nexusAuditLog: auditTable } = await import('../store/schema/nexus-schema.js');
-    const { randomUUID } = await import('node:crypto');
-    const { inArray, sql } = await import('drizzle-orm');
-    const db = await getNexusDb();
-    const allRows = (await db
+    const { getNexusRegistryDb, getNexusRegistryDbPath } = await import('../store/nexus-sqlite.js');
+    const { projectRegistry: regTable, projectIdAliases: aliasTable, projectPaths: pathTable, nexusAuditLog: auditTable, } = await import('../store/schema/nexus-schema.js');
+    // T12324: the registry lives in the GLOBAL store. Opening it directly (not
+    // through the project handle's ATTACH) makes `VACUUM` compact the store the
+    // rows were deleted from.
+    const cleoHome = getCleoHome();
+    const storePath = getNexusRegistryDbPath(cleoHome);
+    const db = await getNexusRegistryDb(cleoHome);
+    const allRows = db
         .select({
         projectId: regTable.projectId,
         projectPath: regTable.projectPath,
         healthStatus: regTable.healthStatus,
         lastIndexed: regTable.lastIndexed,
     })
-        .from(regTable));
+        .from(regTable)
+        .all();
     const pollutedIds = new Set();
     if (opts.matchPolluted) {
         // Group rows by canonicalProjectId. The canonical ID uses git-root+realpath
@@ -141,11 +156,61 @@ export async function cleanProjects(opts) {
             }
         }
     }
-    const matches = allRows.filter((row) => matchesCriteria(row.projectPath, row.healthStatus, row.lastIndexed) ||
-        pollutedIds.has(row.projectId));
+    const registryIds = new Set(allRows.map((row) => row.projectId));
+    const aliasRows = db
+        .select({ legacyId: aliasTable.legacyId, canonicalId: aliasTable.canonicalId })
+        .from(aliasTable)
+        .all();
+    const classification = {
+        total: allRows.length,
+        missingPath: 0,
+        tempPath: 0,
+        testPath: 0,
+        stale: 0,
+        retained: 0,
+        aliases: aliasRows.length,
+        orphanAliases: aliasRows.filter((alias) => !registryIds.has(alias.canonicalId)).length,
+    };
+    const matchedByReason = {};
+    const removals = [];
+    for (const row of allRows) {
+        const missing = !existsSync(row.projectPath);
+        const temp = isTempPath(row.projectPath);
+        const test = isTestPath(row.projectPath);
+        if (missing)
+            classification.missingPath++;
+        if (temp)
+            classification.tempPath++;
+        if (test)
+            classification.testPath++;
+        if (missing || temp || test)
+            classification.stale++;
+        const reasons = [];
+        const normalizedProjectPath = portablePathForMatch(row.projectPath);
+        if (patternRegex?.test(row.projectPath) || patternRegex?.test(normalizedProjectPath))
+            reasons.push('pattern');
+        if (opts.includeTemp && temp)
+            reasons.push('temp-path');
+        if (opts.includeTests && test)
+            reasons.push('test-path');
+        if (opts.matchUnhealthy && row.healthStatus === 'unhealthy')
+            reasons.push('unhealthy');
+        if (opts.matchNeverIndexed && row.lastIndexed === null)
+            reasons.push('never-indexed');
+        if (opts.matchOrphaned && missing)
+            reasons.push('missing-path');
+        if (pollutedIds.has(row.projectId))
+            reasons.push('path-divergent-duplicate');
+        if (reasons.length === 0)
+            continue;
+        for (const reason of reasons)
+            matchedByReason[reason] = (matchedByReason[reason] ?? 0) + 1;
+        removals.push({ projectId: row.projectId, projectPath: row.projectPath, reasons });
+    }
+    classification.retained = classification.total - classification.stale;
     const totalCount = allRows.length;
-    const matched = matches.length;
-    const sample = matches.slice(0, 10).map((r) => path.resolve(r.projectPath));
+    const matched = removals.length;
+    const sample = removals.slice(0, 10).map((r) => path.resolve(r.projectPath));
     if (opts.dryRun || matched === 0) {
         return {
             dryRun: opts.dryRun,
@@ -154,10 +219,12 @@ export async function cleanProjects(opts) {
             remaining: totalCount,
             sample,
             totalCount,
+            classification,
+            matchedByReason,
         };
     }
     // Write audit JSONL before deletion (T9149 matchPolluted mode)
-    if (opts.matchPolluted && opts.auditLog && matches.length > 0) {
+    if (opts.matchPolluted && opts.auditLog && removals.length > 0) {
         try {
             const { appendFile: appendFn, mkdir: mkdirFn } = await import('node:fs/promises');
             const { homedir } = await import('node:os');
@@ -165,7 +232,7 @@ export async function cleanProjects(opts) {
             const auditDir = path.join(homedir(), '.local', 'state', 'cleo');
             await mkdirFn(auditDir, { recursive: true });
             const auditPath = path.join(auditDir, `nexus-cleanup-${ts}.jsonl`);
-            const records = matches
+            const records = removals
                 .map((r) => JSON.stringify({
                 ts: new Date().toISOString(),
                 projectId: r.projectId,
@@ -179,14 +246,50 @@ export async function cleanProjects(opts) {
             // audit is best-effort
         }
     }
-    // Delete matched rows in chunks to keep SQL parameter counts safe (default
-    // SQLite limit is 999 bound variables per statement).
-    const CHUNK = 500;
-    const idsToDelete = matches.map((r) => r.projectId);
-    for (let i = 0; i < idsToDelete.length; i += CHUNK) {
-        const slice = idsToDelete.slice(i, i + CHUNK);
-        await db.delete(regTable).where(inArray(regTable.projectId, slice));
-    }
+    // Rows, their aliases, pre-existing orphan aliases, and the audit receipt
+    // commit together or not at all. Chunked to keep SQL parameter counts safe
+    // (default SQLite limit is 999 bound variables per statement).
+    const CHUNK = 400;
+    const idsToDelete = removals.map((r) => r.projectId);
+    const auditId = randomUUID();
+    const { aliasesRemoved, orphanAliasesRemoved } = db.transaction((tx) => {
+        let purgedAliases = 0;
+        for (let i = 0; i < idsToDelete.length; i += CHUNK) {
+            const slice = idsToDelete.slice(i, i + CHUNK);
+            tx.delete(regTable).where(inArray(regTable.projectId, slice)).run();
+            purgedAliases += Number(tx.delete(aliasTable).where(inArray(aliasTable.canonicalId, slice)).run().changes);
+        }
+        // T12354: path-map rows go with their project, and none may outlive it.
+        tx.run(sql `DELETE FROM ${pathTable} WHERE ${pathTable.projectId} NOT IN (SELECT ${regTable.projectId} FROM ${regTable})`);
+        const orphans = Number(tx.run(sql `DELETE FROM ${aliasTable} WHERE ${aliasTable.canonicalId} NOT IN (SELECT ${regTable.projectId} FROM ${regTable})`).changes);
+        tx.insert(auditTable)
+            .values({
+            id: auditId,
+            action: 'projects.clean',
+            domain: 'nexus',
+            operation: 'projects.clean',
+            success: 1,
+            detailsJson: JSON.stringify({
+                pattern: opts.pattern ?? null,
+                presets: {
+                    includeTemp: opts.includeTemp,
+                    includeTests: opts.includeTests,
+                    matchUnhealthy: opts.matchUnhealthy,
+                    matchNeverIndexed: opts.matchNeverIndexed,
+                    matchOrphaned: opts.matchOrphaned,
+                    removeFs: opts.removeFs,
+                    vacuum: opts.vacuum,
+                },
+                count: matched,
+                aliasesRemoved: purgedAliases,
+                orphanAliasesRemoved: orphans,
+                sample,
+                removed: removals,
+            }),
+        })
+            .run();
+        return { aliasesRemoved: purgedAliases, orphanAliasesRemoved: orphans };
+    }, { behavior: 'immediate' });
     const remaining = totalCount - matched;
     // Optional filesystem cleanup — runs only after the row has been purged so a
     // partial failure leaves no DB→disk drift (worst case: dir lingers, can be
@@ -196,7 +299,7 @@ export async function cleanProjects(opts) {
     if (opts.removeFs) {
         fsRemoved = 0;
         fsFailed = 0;
-        for (const row of matches) {
+        for (const row of removals) {
             const p = row.projectPath;
             // Refuse to delete suspiciously short or root-ish paths even if the DB
             // says so. Anything < 8 chars or with fewer than 3 path segments under
@@ -220,54 +323,31 @@ export async function cleanProjects(opts) {
             }
         }
     }
-    // Optional VACUUM to reclaim disk space after large purges.
+    // Optional VACUUM of the GLOBAL registry store after large purges. The WAL
+    // is checkpointed so the file on disk actually shrinks.
+    let vacuum;
     let vacuumBytesFreed;
     if (opts.vacuum) {
-        let beforeBytes = 0;
-        let afterBytes = 0;
         try {
-            const { statSync: stat } = await import('node:fs');
-            const { getNexusDbPath } = await import('../store/nexus-sqlite.js');
-            const dbPath = getNexusDbPath();
-            beforeBytes = stat(dbPath).size;
-            await db.run(sql `VACUUM`);
-            afterBytes = stat(dbPath).size;
+            const beforeBytes = storeBytes(db);
+            db.run(sql `VACUUM`);
+            db.run(sql `PRAGMA wal_checkpoint(TRUNCATE)`);
+            const afterBytes = storeBytes(db);
+            vacuum = { beforeBytes, afterBytes };
             vacuumBytesFreed = Math.max(0, beforeBytes - afterBytes);
         }
         catch {
             vacuumBytesFreed = 0;
         }
     }
-    // Audit log (best-effort)
-    try {
-        await db.insert(auditTable).values({
-            id: randomUUID(),
-            action: 'projects.clean',
-            domain: 'nexus',
-            operation: 'projects.clean',
-            success: 1,
-            detailsJson: JSON.stringify({
-                pattern: opts.pattern ?? null,
-                presets: {
-                    includeTemp: opts.includeTemp,
-                    includeTests: opts.includeTests,
-                    matchUnhealthy: opts.matchUnhealthy,
-                    matchNeverIndexed: opts.matchNeverIndexed,
-                    matchOrphaned: opts.matchOrphaned,
-                    removeFs: opts.removeFs,
-                    vacuum: opts.vacuum,
-                },
-                count: matched,
-                fsRemoved,
-                fsFailed,
-                vacuumBytesFreed,
-                sample,
-            }),
-        });
-    }
-    catch {
-        // Audit failure is non-fatal
-    }
+    const receipt = {
+        auditId,
+        storePath,
+        removed: removals,
+        aliasesRemoved,
+        orphanAliasesRemoved,
+        ...(vacuum !== undefined ? { vacuum } : {}),
+    };
     return {
         dryRun: false,
         matched,
@@ -275,6 +355,9 @@ export async function cleanProjects(opts) {
         remaining,
         sample,
         totalCount,
+        classification,
+        matchedByReason,
+        receipt,
         ...(fsRemoved !== undefined ? { fsRemoved } : {}),
         ...(fsFailed !== undefined ? { fsFailed } : {}),
         ...(vacuumBytesFreed !== undefined ? { vacuumBytesFreed } : {}),

package/dist/nexus/projects-clean.js.map

@@ -1 +1 @@
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package/dist/nexus/query.d.ts.map

@@ -1 +1 @@
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package/dist/nexus/query.js

@@ -20,6 +20,7 @@ import { getTaskAccessor } from '../store/data-accessor.js';
 import { getBrainNativeDb } from '../store/memory-sqlite.js';
 import { getNexusNativeDb } from '../store/nexus-sqlite.js';
 import { nexusGetProject, readRegistry } from './registry.js';
+import { registryStorePath } from './registry-hygiene.js';
 // ── Query syntax ─────────────────────────────────────────────────────
 /** Regex for a bare task ID (T followed by 3+ digits). */
 const TASK_ID_RE = /^T\d{3,}$/;
@@ -118,14 +119,14 @@ export async function resolveProjectPath(projectName) {
  * Read tasks from a project's task database.
  */
 async function readProjectTasks(projectPath) {
-    const tasksDbPath = join(projectPath, '.cleo', 'tasks.db');
+    const storePath = registryStorePath(projectPath);
     try {
         const accessor = await getTaskAccessor(projectPath);
         const { tasks } = await accessor.queryTasks({});
         return tasks;
     }
     catch {
-        throw new CleoError(ExitCode.NOT_FOUND, `Project task data not found: ${tasksDbPath}`);
+        throw new CleoError(ExitCode.NOT_FOUND, `Project task data not found: ${storePath}`);
     }
 }
 export async function resolveTask(projectRootOrQuery, paramsOrCurrentProject) {

package/dist/nexus/query.js.map

@@ -1 +1 @@
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