@cleocode/core 2026.9.19 → 2026.9.21

package/dist/doctor/worktree-stores.d.ts

@@ -0,0 +1,128 @@
+/**
+ * Detect project stores stranded inside CLEO worktrees (T12460).
+ *
+ * ## The failure this reports
+ *
+ * Before T12460, a `cleo` command run inside an orchestrate worktree
+ * (`<cleoHome>/worktrees/<projectHash>/<taskId>/`) resolved the WORKTREE's own
+ * `.cleo/` as the project directory: the nearest-`.cleo` walk (and the
+ * `CLEO_WORKTREE_ROOT` scope) won before the gitlink step. The worktree store
+ * opened empty, `autoRecoverFromBackup` copied the parent project's newest
+ * snapshot into it (~1.25 GB on this repo), and `createSafetyBackup` added a
+ * same-size `.bak` beside it. Every later write from that worktree landed in the
+ * copy. Nothing merges it back, and worktree prune deletes or quarantines it.
+ *
+ * Path resolution now maps a worktree to its parent project's store, so no new
+ * copies are created. Copies made before the fix are still on disk and may hold
+ * the only record of writes made from inside the worktree. This scan finds them
+ * and reports, per table, whether a copy holds rows the parent does not.
+ *
+ * ## Read-only contract
+ *
+ * Nothing is deleted, moved, or written. Every SQLite file is opened with
+ * `readOnly: true`. To import rows a copy holds that the parent lacks, use
+ * `cleo doctor split-brain --source <copy>` after reviewing this report.
+ *
+ * @task T12460
+ * @see ADR-055 — worktree-by-default
+ */
+/** Per-table comparison of a stranded copy against the parent store. */
+export interface WorktreeStoreTableDiff {
+    /** Table name, e.g. `tasks_tasks`. */
+    readonly table: string;
+    /** Rows in the stranded copy. */
+    readonly rowsInCopy: number;
+    /** Rows of the copy whose primary key is ABSENT from the parent table. */
+    readonly missingInParent: number;
+    /**
+     * Rows present in both whose timestamp in the copy is later than the parent's
+     * timestamp for the SAME key: updates made in the worktree that the parent's
+     * version of the row does not reflect.
+     */
+    readonly newerThanParent: number;
+    /** Newest timestamp in the copy's column, or `null` when the table is empty. */
+    readonly newestInCopy: string | null;
+    /** Newest timestamp in the parent's column, or `null` when the table is empty. */
+    readonly newestInParent: string | null;
+}
+/** One database-like file found under a worktree's `.cleo/`. */
+export interface WorktreeStoreFile {
+    /** Absolute path of the file. */
+    readonly path: string;
+    /** Bare file name, e.g. `cleo.db` or `cleo-pre-cleo.db.bak`. */
+    readonly name: string;
+    /** Size in bytes. */
+    readonly sizeBytes: number;
+    /** Last modification time, ISO 8601. */
+    readonly modifiedAt: string;
+    /** Whether the file carries the SQLite 3 header. */
+    readonly isSqlite: boolean;
+    /**
+     * `true` when at least one compared table holds a row the parent lacks by
+     * key, or one newer than the parent's newest; `false` when every compared
+     * table is covered by the parent; `null` when no comparison was possible.
+     */
+    readonly hasRowsNewerThanParent: boolean | null;
+    /** Per-table comparison; empty when no comparison was possible. */
+    readonly tables: readonly WorktreeStoreTableDiff[];
+    /** Why the comparison was skipped or failed, when it was. */
+    readonly note?: string;
+}
+/** One worktree whose `.cleo/` holds at least one store file. */
+export interface WorktreeStoreEntry {
+    /** Absolute worktree path. */
+    readonly worktreePath: string;
+    /** Whether git still lists the worktree (`git worktree list`). */
+    readonly registeredWithGit: boolean;
+    /** Store files found directly under `<worktree>/.cleo/`. */
+    readonly files: readonly WorktreeStoreFile[];
+}
+/** Result of {@link scanWorktreeStores}. */
+export interface WorktreeStoreScanResult {
+    /** Absolute parent project root that was scanned. */
+    readonly projectRoot: string;
+    /** Absolute path of the parent project's store. */
+    readonly parentStorePath: string;
+    /** Whether the parent store exists; comparisons are skipped when it does not. */
+    readonly parentStoreExists: boolean;
+    /** Canonical worktree directory for this project (`<cleoHome>/worktrees/<hash>`). */
+    readonly worktreeBase: string;
+    /** Number of worktree directories inspected. */
+    readonly worktreesScanned: number;
+    /** Worktrees holding store files, sorted by path. */
+    readonly entries: readonly WorktreeStoreEntry[];
+    /** Total store files found across all worktrees. */
+    readonly strandedFileCount: number;
+    /** Total bytes those files occupy. */
+    readonly strandedBytes: number;
+    /** Paths of files that hold rows the parent store does not. */
+    readonly filesWithNewerRows: readonly string[];
+}
+/** Options for {@link scanWorktreeStores}. */
+export interface WorktreeStoreScanOptions {
+    /** Override the canonical worktree base (tests). */
+    readonly worktreeBase?: string;
+    /** Skip row comparisons; list files only. Default `false`. */
+    readonly skipCompare?: boolean;
+}
+/**
+ * Find project stores stranded inside the worktrees of `projectRoot`.
+ *
+ * Worktrees are discovered from both `git worktree list` and the canonical
+ * worktree base, so a worktree git no longer tracks is still inspected. For
+ * each, every database-like file directly under `<worktree>/.cleo/` is listed;
+ * SQLite files are compared against the parent's `.cleo/cleo.db` table by table.
+ *
+ * @param projectRoot - Parent project root (the main checkout).
+ * @param options - Optional worktree-base override and compare switch.
+ * @returns The scan result. Never throws for a missing directory or unreadable file.
+ * @remarks Strictly read-only: nothing is created, moved, or deleted.
+ * @example
+ * ```ts
+ * const result = scanWorktreeStores('/home/u/project');
+ * for (const path of result.filesWithNewerRows) console.log(path);
+ * ```
+ * @task T12460
+ */
+export declare function scanWorktreeStores(projectRoot: string, options?: WorktreeStoreScanOptions): WorktreeStoreScanResult;
+//# sourceMappingURL=worktree-stores.d.ts.map

package/dist/doctor/worktree-stores.d.ts.map

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package/dist/doctor/worktree-stores.js

@@ -0,0 +1,374 @@
+/**
+ * Detect project stores stranded inside CLEO worktrees (T12460).
+ *
+ * ## The failure this reports
+ *
+ * Before T12460, a `cleo` command run inside an orchestrate worktree
+ * (`<cleoHome>/worktrees/<projectHash>/<taskId>/`) resolved the WORKTREE's own
+ * `.cleo/` as the project directory: the nearest-`.cleo` walk (and the
+ * `CLEO_WORKTREE_ROOT` scope) won before the gitlink step. The worktree store
+ * opened empty, `autoRecoverFromBackup` copied the parent project's newest
+ * snapshot into it (~1.25 GB on this repo), and `createSafetyBackup` added a
+ * same-size `.bak` beside it. Every later write from that worktree landed in the
+ * copy. Nothing merges it back, and worktree prune deletes or quarantines it.
+ *
+ * Path resolution now maps a worktree to its parent project's store, so no new
+ * copies are created. Copies made before the fix are still on disk and may hold
+ * the only record of writes made from inside the worktree. This scan finds them
+ * and reports, per table, whether a copy holds rows the parent does not.
+ *
+ * ## Read-only contract
+ *
+ * Nothing is deleted, moved, or written. Every SQLite file is opened with
+ * `readOnly: true`. To import rows a copy holds that the parent lacks, use
+ * `cleo doctor split-brain --source <copy>` after reviewing this report.
+ *
+ * @task T12460
+ * @see ADR-055 — worktree-by-default
+ */
+import { closeSync, existsSync, openSync, readdirSync, readSync, realpathSync, statSync, } from 'node:fs';
+import { join, resolve } from 'node:path';
+import { DatabaseSync } from 'node:sqlite';
+import { pathToFileURL } from 'node:url';
+import { computeProjectHash, resolveWorktreeRootForHash } from '@cleocode/paths';
+import { listRegisteredWorktrees } from '@cleocode/worktree';
+/** File name of the consolidated project store. */
+const PROJECT_STORE_FILENAME = 'cleo.db';
+/** First 16 bytes of every SQLite 3 database file. */
+const SQLITE_HEADER = 'SQLite format 3\u0000';
+/**
+ * Tables compared between a stranded copy and the parent store, each with the
+ * single-column primary key and the timestamp column that best reflects a write.
+ */
+const COMPARED_TABLES = [
+    { table: 'tasks_tasks', key: 'id', time: 'updated_at' },
+    { table: 'tasks_sessions', key: 'id', time: 'started_at' },
+    { table: 'tasks_audit_log', key: 'id', time: 'timestamp' },
+    { table: 'tasks_lifecycle_evidence', key: 'id', time: 'recorded_at' },
+    { table: 'pipeline_manifest', key: 'id', time: 'created_at' },
+    { table: 'brain_observations', key: 'id', time: 'created_at' },
+    { table: 'brain_decisions', key: 'id', time: 'created_at' },
+    { table: 'brain_learnings', key: 'id', time: 'created_at' },
+    { table: 'brain_patterns', key: 'id', time: 'extracted_at' },
+    { table: 'conduit_messages', key: 'id', time: 'created_at' },
+];
+/**
+ * Canonicalise a path through symlinks so git's spelling and the directory
+ * listing's spelling of one worktree compare equal.
+ *
+ * @param p - Path to canonicalise.
+ * @returns The real path, or the resolved path when it does not exist.
+ */
+function canonicalPath(p) {
+    try {
+        return realpathSync(p);
+    }
+    catch {
+        return resolve(p);
+    }
+}
+/**
+ * List linked worktrees of `projectRoot` through the `@cleocode/worktree` registry reader.
+ *
+ * @param projectRoot - Main repository root.
+ * @returns Absolute worktree paths, excluding the main checkout itself.
+ */
+function listGitLinkedWorktrees(projectRoot) {
+    const main = canonicalPath(projectRoot);
+    return listRegisteredWorktrees(projectRoot)
+        .map((wt) => canonicalPath(wt.path))
+        .filter((p) => p !== main);
+}
+/**
+ * List child directories of the canonical worktree base.
+ *
+ * @param base - `<cleoHome>/worktrees/<projectHash>`.
+ * @returns Absolute child directory paths; empty when the base is absent.
+ */
+function listCanonicalWorktreeDirs(base) {
+    if (!existsSync(base))
+        return [];
+    try {
+        return readdirSync(base, { withFileTypes: true })
+            .filter((d) => d.isDirectory())
+            .map((d) => canonicalPath(join(base, d.name)));
+    }
+    catch {
+        return [];
+    }
+}
+/**
+ * Report whether a file begins with the SQLite 3 header.
+ *
+ * @param path - File to probe.
+ * @returns `true` for a SQLite database file.
+ */
+function hasSqliteHeader(path) {
+    let fd;
+    try {
+        fd = openSync(path, 'r');
+        const buf = Buffer.alloc(SQLITE_HEADER.length);
+        const read = readSync(fd, buf, 0, buf.length, 0);
+        return read === buf.length && buf.toString('latin1') === SQLITE_HEADER;
+    }
+    catch {
+        return false;
+    }
+    finally {
+        if (fd !== undefined)
+            closeSync(fd);
+    }
+}
+/**
+ * Open a SQLite file for inspection without leaving anything behind on disk.
+ *
+ * A plain read-only open of a WAL-mode file creates `-wal`/`-shm` sidecars that
+ * a read-only connection cannot remove. When no `-wal` exists there is nothing
+ * uncheckpointed to read, so the file is opened `immutable=1`, which creates no
+ * sidecar at all. When a `-wal` exists it holds committed rows the main file
+ * lacks, so the file is opened read-only through the normal path to include them.
+ *
+ * @param path - SQLite file to open.
+ * @returns A read-only handle.
+ */
+function openForInspection(path) {
+    let hasWal = false;
+    try {
+        hasWal = statSync(`${path}-wal`).size > 0;
+    }
+    catch {
+        hasWal = false;
+    }
+    if (hasWal) {
+        // db-open-allowed: read-only forensic probe; a chokepoint open would run migrations and take a writer lease for a report
+        return new DatabaseSync(path, { readOnly: true }); // db-open-allowed: read-only forensic probe
+    }
+    const url = pathToFileURL(path);
+    url.searchParams.set('immutable', '1');
+    // db-open-allowed: read-only forensic probe; immutable so no sidecar is created beside a stranded copy
+    return new DatabaseSync(url, { readOnly: true }); // db-open-allowed: read-only forensic probe
+}
+/**
+ * Report whether a table and both named columns exist in `db`.
+ *
+ * @param db - Open handle.
+ * @param table - Table name.
+ * @param columns - Columns that must exist.
+ * @returns `true` when the table carries every column.
+ */
+function hasColumns(db, table, columns) {
+    try {
+        const cols = db.prepare(`PRAGMA table_info("${table}")`).all();
+        const names = new Set(cols.map((c) => c.name));
+        return columns.every((c) => names.has(c));
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Coerce a SQLite scalar to a display string.
+ *
+ * @param value - Scalar from a `MAX()` aggregate.
+ * @returns String form, or `null` for SQL NULL.
+ */
+function scalarToString(value) {
+    if (value === null || value === undefined)
+        return null;
+    return String(value);
+}
+/**
+ * Compare one table of a stranded copy against the parent store.
+ *
+ * @param copy - Read-only handle on the stranded copy.
+ * @param parent - Read-only handle on the parent store.
+ * @param spec - Table, key and timestamp column.
+ * @returns The diff, or `null` when either side lacks the table or columns.
+ */
+function compareTable(copy, parent, spec) {
+    const { table, key, time } = spec;
+    if (!hasColumns(copy, table, [key, time]) || !hasColumns(parent, table, [key, time]))
+        return null;
+    const parentNewestRaw = parent.prepare(`SELECT MAX("${time}") AS newest FROM "${table}"`).get().newest;
+    const copyNewestRaw = copy.prepare(`SELECT MAX("${time}") AS newest FROM "${table}"`).get().newest;
+    const parentTimes = new Map();
+    for (const row of parent
+        .prepare(`SELECT "${key}" AS k, "${time}" AS t FROM "${table}"`)
+        .iterate()) {
+        parentTimes.set(String(row.k), row.t);
+    }
+    let rowsInCopy = 0;
+    let missingInParent = 0;
+    let newerThanParent = 0;
+    for (const row of copy
+        .prepare(`SELECT "${key}" AS k, "${time}" AS t FROM "${table}"`)
+        .iterate()) {
+        rowsInCopy++;
+        const k = String(row.k);
+        if (!parentTimes.has(k)) {
+            missingInParent++;
+            continue;
+        }
+        const parentTime = parentTimes.get(k) ?? null;
+        if (row.t !== null && (parentTime === null || row.t > parentTime))
+            newerThanParent++;
+    }
+    return {
+        table,
+        rowsInCopy,
+        missingInParent,
+        newerThanParent,
+        newestInCopy: scalarToString(copyNewestRaw),
+        newestInParent: scalarToString(parentNewestRaw),
+    };
+}
+/**
+ * Compare a stranded SQLite copy against the parent store, read-only.
+ *
+ * @param copyPath - Stranded copy.
+ * @param parent - Read-only parent handle, or `null` when the parent is absent.
+ * @returns Per-table diffs plus the aggregate verdict and an optional note.
+ */
+function compareCopy(copyPath, parent) {
+    if (parent === null) {
+        return { hasRowsNewerThanParent: null, tables: [], note: 'parent store not found' };
+    }
+    let copy;
+    try {
+        const handle = openForInspection(copyPath);
+        copy = handle;
+        const tables = COMPARED_TABLES.map((spec) => compareTable(handle, parent, spec)).filter((d) => d !== null);
+        if (tables.length === 0) {
+            return { hasRowsNewerThanParent: null, tables, note: 'no comparable tables' };
+        }
+        return {
+            hasRowsNewerThanParent: tables.some((t) => t.missingInParent > 0 || t.newerThanParent > 0),
+            tables,
+        };
+    }
+    catch (err) {
+        return {
+            hasRowsNewerThanParent: null,
+            tables: [],
+            note: `comparison failed: ${err instanceof Error ? err.message : String(err)}`,
+        };
+    }
+    finally {
+        copy?.close();
+    }
+}
+/**
+ * Report whether a `.cleo/` entry name looks like a database or database backup.
+ *
+ * @param name - File name.
+ * @returns `true` for `*.db`, `*.bak` and `*.db.*` files other than WAL/SHM sidecars.
+ */
+function isStoreLikeName(name) {
+    if (name.endsWith('-wal') || name.endsWith('-shm') || name.endsWith('-journal'))
+        return false;
+    return name.endsWith('.db') || name.endsWith('.bak') || name.includes('.db.');
+}
+/**
+ * Find project stores stranded inside the worktrees of `projectRoot`.
+ *
+ * Worktrees are discovered from both `git worktree list` and the canonical
+ * worktree base, so a worktree git no longer tracks is still inspected. For
+ * each, every database-like file directly under `<worktree>/.cleo/` is listed;
+ * SQLite files are compared against the parent's `.cleo/cleo.db` table by table.
+ *
+ * @param projectRoot - Parent project root (the main checkout).
+ * @param options - Optional worktree-base override and compare switch.
+ * @returns The scan result. Never throws for a missing directory or unreadable file.
+ * @remarks Strictly read-only: nothing is created, moved, or deleted.
+ * @example
+ * ```ts
+ * const result = scanWorktreeStores('/home/u/project');
+ * for (const path of result.filesWithNewerRows) console.log(path);
+ * ```
+ * @task T12460
+ */
+export function scanWorktreeStores(projectRoot, options = {}) {
+    const root = canonicalPath(projectRoot);
+    const parentStorePath = join(root, '.cleo', PROJECT_STORE_FILENAME);
+    const parentStoreExists = existsSync(parentStorePath);
+    const worktreeBase = options.worktreeBase ?? resolveWorktreeRootForHash(computeProjectHash(root));
+    const registered = new Set(listGitLinkedWorktrees(root));
+    const candidates = new Set([...registered, ...listCanonicalWorktreeDirs(worktreeBase)]);
+    candidates.delete(root);
+    let parent = null;
+    if (parentStoreExists && options.skipCompare !== true) {
+        try {
+            parent = openForInspection(parentStorePath);
+        }
+        catch {
+            parent = null;
+        }
+    }
+    const entries = [];
+    try {
+        for (const worktreePath of [...candidates].sort()) {
+            const cleoDir = join(worktreePath, '.cleo');
+            if (!existsSync(cleoDir))
+                continue;
+            let names;
+            try {
+                names = readdirSync(cleoDir).filter(isStoreLikeName).sort();
+            }
+            catch {
+                continue;
+            }
+            const files = [];
+            for (const name of names) {
+                const path = join(cleoDir, name);
+                let stat;
+                try {
+                    stat = statSync(path);
+                }
+                catch {
+                    continue;
+                }
+                if (!stat.isFile())
+                    continue;
+                const isSqlite = hasSqliteHeader(path);
+                const comparison = options.skipCompare === true
+                    ? { hasRowsNewerThanParent: null, tables: [], note: 'comparison skipped' }
+                    : isSqlite
+                        ? compareCopy(path, parent)
+                        : { hasRowsNewerThanParent: null, tables: [], note: 'not a SQLite database' };
+                files.push({
+                    path,
+                    name,
+                    sizeBytes: stat.size,
+                    modifiedAt: stat.mtime.toISOString(),
+                    isSqlite,
+                    ...comparison,
+                });
+            }
+            if (files.length > 0) {
+                entries.push({
+                    worktreePath,
+                    registeredWithGit: registered.has(worktreePath),
+                    files,
+                });
+            }
+        }
+    }
+    finally {
+        parent?.close();
+    }
+    const allFiles = entries.flatMap((e) => e.files);
+    return {
+        projectRoot: root,
+        parentStorePath,
+        parentStoreExists,
+        worktreeBase,
+        worktreesScanned: candidates.size,
+        entries,
+        strandedFileCount: allFiles.length,
+        strandedBytes: allFiles.reduce((sum, f) => sum + f.sizeBytes, 0),
+        filesWithNewerRows: allFiles
+            .filter((f) => f.hasRowsNewerThanParent === true)
+            .map((f) => f.path),
+    };
+}
+//# sourceMappingURL=worktree-stores.js.map

package/dist/doctor/worktree-stores.js.map

@@ -0,0 +1 @@
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package/dist/engine/engine-ops.d.ts.map

@@ -1 +1 @@
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