@cleocode/core 2026.4.30 → 2026.4.35

package/dist/store/backup-unpack.js

@@ -0,0 +1,449 @@
+/**
+ * backup-unpack.ts — Bundle extraction and integrity verification for .cleobundle.tar.gz.
+ *
+ * Implements the unpack + verify half of the T311 import lifecycle.
+ * Extracts a .cleobundle.tar.gz (or .enc.cleobundle.tar.gz) to a staging
+ * directory and verifies all 6 integrity layers defined in ADR-038 §4.2.
+ *
+ * The caller is responsible for cleaning up the staging directory via
+ * {@link cleanupStaging} after processing. Restore-to-disk is the
+ * responsibility of T361 (CLI import handler).
+ *
+ * Verification layers (executed in strict order):
+ *   Layer 1 — AES-256-GCM auth tag (encrypted bundles only)
+ *   Layer 2 — Manifest self-hash (SHA-256 with placeholder substitution)
+ *   Layer 3 — Manifest JSON Schema validation (bundled schemas/manifest-v1.json)
+ *   Layer 4 — Per-file SHA-256 checksums
+ *   Layer 5 — SQLite PRAGMA integrity_check
+ *   Layer 6 — Schema version comparison (warnings only, never blocks)
+ *
+ * @task T350
+ * @epic T311
+ * @why ADR-038 — the unpack + verify half of the T311 import lifecycle.
+ *      Restore-to-disk is the responsibility of T361 (CLI import handler);
+ *      this module stops after verification and returns a staging dir path.
+ * @module store/backup-unpack
+ */
+import crypto from 'node:crypto';
+import fs from 'node:fs';
+import { createRequire } from 'node:module';
+import os from 'node:os';
+import path from 'node:path';
+// ajv/dist/2020 provides JSON Schema Draft 2020-12 support required by
+// schemas/manifest-v1.json which declares `"$schema": "https://json-schema.org/draft/2020-12/schema"`.
+import { default as Ajv2020Import } from 'ajv/dist/2020.js';
+import { default as addFormatsImport } from 'ajv-formats';
+import { extract as tarExtract } from 'tar';
+import { decryptBundle, isEncryptedBundle } from './backup-crypto.js';
+// ---------------------------------------------------------------------------
+// node:sqlite interop (createRequire — Vitest strips `node:` prefix)
+// ---------------------------------------------------------------------------
+const _require = createRequire(import.meta.url);
+const { DatabaseSync } = _require('node:sqlite');
+// ---------------------------------------------------------------------------
+// ajv ESM/CJS interop — Draft 2020-12 variant
+// ---------------------------------------------------------------------------
+const ajv2020Mod = Ajv2020Import;
+const Ajv2020 = (typeof ajv2020Mod.default === 'function' ? ajv2020Mod.default : Ajv2020Import);
+const fmtMod = addFormatsImport;
+const addFormats = (typeof fmtMod.default === 'function' ? fmtMod.default : addFormatsImport);
+// ---------------------------------------------------------------------------
+// Exit codes (ADR-038 §4.3)
+// ---------------------------------------------------------------------------
+/**
+ * Error thrown by {@link unpackBundle} when any integrity layer fails.
+ *
+ * Exit codes:
+ * - `70` `E_BUNDLE_DECRYPT`     — decryption or passphrase failure
+ * - `71` `E_BUNDLE_SCHEMA`      — manifest.json failed JSON Schema validation
+ * - `72` `E_CHECKSUM_MISMATCH`  — SHA-256 checksum did not match
+ * - `73` `E_SQLITE_INTEGRITY`   — SQLite PRAGMA integrity_check failed
+ * - `74` `E_MANIFEST_MISSING`   — manifest.json absent from archive
+ * - `75` `E_SCHEMAS_MISSING`    — schemas/manifest-v1.json absent from archive
+ *
+ * @task T350
+ * @epic T311
+ */
+export class BundleError extends Error {
+    code;
+    codeName;
+    /**
+     * @param code     - Numeric exit code (70–75).
+     * @param codeName - Symbolic constant name, e.g. `'E_BUNDLE_DECRYPT'`.
+     * @param message  - Human-readable error description.
+     */
+    constructor(code, codeName, message) {
+        super(message);
+        this.code = code;
+        this.codeName = codeName;
+        this.name = 'BundleError';
+    }
+}
+// ---------------------------------------------------------------------------
+// Private helpers
+// ---------------------------------------------------------------------------
+/** Compute SHA-256 hex of a buffer. */
+function sha256OfBuffer(buf) {
+    return crypto.createHash('sha256').update(buf).digest('hex');
+}
+/** Compute SHA-256 hex of a file on disk. */
+function sha256OfFile(filePath) {
+    return sha256OfBuffer(fs.readFileSync(filePath));
+}
+/**
+ * Build and return a singleton Ajv 2020-12 instance with formats support.
+ * The schema cache lives for the lifetime of the process, which is acceptable
+ * since the manifest-v1.json schema is stable.
+ */
+let _ajv2020 = null;
+function getAjv2020() {
+    if (_ajv2020 === null) {
+        _ajv2020 = new Ajv2020({ allErrors: true, strict: false, allowUnionTypes: true });
+        addFormats(_ajv2020);
+    }
+    return _ajv2020;
+}
+/**
+ * Stable schema ID for manifest-v1.json used as Ajv internal key.
+ * Having a fixed, well-known ID lets us call `ajv.getSchema(id)` on
+ * subsequent requests instead of re-compiling from disk every time.
+ */
+const MANIFEST_SCHEMA_ID = 'cleo-manifest-v1-internal';
+/**
+ * Validate `data` against the JSON Schema loaded from `schemaPath`.
+ * Returns an array of error messages; empty array means valid.
+ *
+ * Uses a stable internal schema ID so that multiple calls within the
+ * same process reuse the compiled validator without triggering the Ajv
+ * "schema already exists" error.
+ */
+function validateAgainstJsonSchema(data, schemaPath) {
+    const ajv = getAjv2020();
+    // Reuse previously compiled validator if already registered.
+    let validate = ajv.getSchema(MANIFEST_SCHEMA_ID);
+    if (validate === undefined) {
+        const rawSchema = JSON.parse(fs.readFileSync(schemaPath, 'utf-8'));
+        // Strip the external `$id` to avoid Ajv's cross-call duplicate-id check,
+        // then add with our stable internal key.
+        const { $id: _unusedId, ...schemaWithoutId } = rawSchema;
+        ajv.addSchema(schemaWithoutId, MANIFEST_SCHEMA_ID);
+        validate = ajv.getSchema(MANIFEST_SCHEMA_ID);
+    }
+    if (validate(data)) {
+        return [];
+    }
+    return (validate.errors ?? []).map((e) => `${e.instancePath ?? '/'}: ${e.message ?? 'unknown'}`);
+}
+/**
+ * Read the latest applied Drizzle migration identifier from a local DB file.
+ *
+ * Looks for a `__drizzle_migrations` or `drizzle_migrations` table and reads
+ * the latest `folder_millis` or `created_at` value. Returns `null` if the
+ * local DB file does not exist or has no migration table (unknown DB).
+ *
+ * @param dbName - Logical database name (e.g. "tasks").
+ * @returns Migration identifier string, or `null` if unknown.
+ */
+function getLocalSchemaVersion(dbName) {
+    // Resolve the path for known project-tier databases relative to this module.
+    // packages/core/src/store/backup-unpack.ts → packages/core/ → packages/ → root
+    const thisFile = import.meta.url.replace('file://', '');
+    const packageRoot = path.resolve(path.dirname(thisFile), '..', '..', '..');
+    // Known DB paths: project-tier DBs live at <projectRoot>/.cleo/<name>.db but
+    // we can only inspect the local running project's DB here.  For schema version
+    // comparison we read from the local .cleo directory relative to a project root
+    // heuristic, but that is inherently environment-specific.  The simpler and
+    // safer approach (spec §9 best-effort) is to look at the Drizzle migration
+    // folder for the known DBs shipped with this package.
+    const migrationCandidates = [
+        path.join(packageRoot, 'migrations', `drizzle-${dbName}`),
+        path.join(packageRoot, 'migrations', dbName),
+    ];
+    for (const dir of migrationCandidates) {
+        if (!fs.existsSync(dir))
+            continue;
+        try {
+            const entries = fs
+                .readdirSync(dir)
+                .filter((n) => /^\d+/.test(n))
+                .sort()
+                .reverse();
+            if (entries.length > 0 && entries[0] != null) {
+                // Strip non-numeric suffix to get the millis part
+                const match = /^(\d+)/.exec(entries[0]);
+                if (match?.[1] != null) {
+                    return match[1];
+                }
+            }
+        }
+        catch {
+            // Non-fatal — fall through to next candidate
+        }
+    }
+    return null;
+}
+/**
+ * Compare bundle schema version vs local schema version for a single DB.
+ * Returns a {@link SchemaCompatWarning} when the versions differ, or `null`.
+ */
+function compareSchemaVersions(dbName, bundleVersion) {
+    if (bundleVersion === 'unknown')
+        return null;
+    const localVersion = getLocalSchemaVersion(dbName);
+    if (localVersion === null)
+        return null; // unknown DB — skip comparison
+    if (localVersion === 'unknown')
+        return null;
+    if (bundleVersion === localVersion)
+        return null;
+    // Numeric comparison where possible (Drizzle uses epoch millis as folder names)
+    const bNum = Number(bundleVersion);
+    const lNum = Number(localVersion);
+    if (!Number.isNaN(bNum) && !Number.isNaN(lNum)) {
+        const severity = bNum < lNum ? 'older-bundle' : 'newer-bundle';
+        return { db: dbName, bundleVersion, localVersion, severity };
+    }
+    // Fallback: lexicographic comparison
+    const severity = bundleVersion < localVersion ? 'older-bundle' : 'newer-bundle';
+    return { db: dbName, bundleVersion, localVersion, severity };
+}
+// ---------------------------------------------------------------------------
+// Public API
+// ---------------------------------------------------------------------------
+/**
+ * Extract a `.cleobundle.tar.gz` to a temp staging directory and verify all
+ * 6 integrity layers in strict sequence (ADR-038 §4.2).
+ *
+ * On any failure AFTER the staging directory is created, the staging directory
+ * is cleaned up before the {@link BundleError} is thrown.
+ *
+ * The caller MUST call {@link cleanupStaging} with the returned `stagingDir`
+ * after it is done processing.
+ *
+ * @param input - Bundle path and optional passphrase.
+ * @returns Verification result with staging dir, manifest, layer flags, and warnings.
+ * @throws {BundleError} On any integrity failure (exit codes 70–75).
+ *
+ * @task T350
+ * @epic T311
+ */
+export async function unpackBundle(input) {
+    const { bundlePath, passphrase } = input;
+    // ----- Step 1: Read bundle header (first 8 bytes) -------------------------
+    const fd = fs.openSync(bundlePath, 'r');
+    const header = Buffer.alloc(8);
+    fs.readSync(fd, header, 0, 8, 0);
+    fs.closeSync(fd);
+    // ----- Step 2: Detect encryption ------------------------------------------
+    const encrypted = isEncryptedBundle(header);
+    // ----- Step 3: Decrypt if needed ------------------------------------------
+    let encryptionAuth = false;
+    let tarPath;
+    let tmpDecryptedPath = null;
+    if (encrypted) {
+        if (!passphrase || passphrase.length === 0) {
+            throw new BundleError(70, 'E_BUNDLE_DECRYPT', 'Bundle is encrypted but no passphrase was provided.');
+        }
+        const encryptedBuf = fs.readFileSync(bundlePath);
+        let decrypted;
+        try {
+            decrypted = decryptBundle(encryptedBuf, passphrase);
+        }
+        catch (err) {
+            const msg = err instanceof Error ? err.message : String(err);
+            throw new BundleError(70, 'E_BUNDLE_DECRYPT', `Decryption failed: ${msg}`);
+        }
+        // Write decrypted tar.gz to a temp file for extraction
+        tmpDecryptedPath = path.join(os.tmpdir(), `cleo-unpack-dec-${Date.now()}.tar.gz`);
+        fs.writeFileSync(tmpDecryptedPath, decrypted);
+        tarPath = tmpDecryptedPath;
+        encryptionAuth = true;
+    }
+    else {
+        tarPath = bundlePath;
+        // unencrypted: auth is N/A — report true (not applicable = pass)
+        encryptionAuth = true;
+    }
+    // ----- Step 4: Create staging directory -----------------------------------
+    const stagingDir = fs.mkdtempSync(path.join(os.tmpdir(), 'cleo-unpack-'));
+    // From here on, any failure must clean up stagingDir (and tmpDecryptedPath).
+    const cleanup = () => {
+        try {
+            fs.rmSync(stagingDir, { recursive: true, force: true });
+        }
+        catch {
+            // best-effort
+        }
+        if (tmpDecryptedPath !== null) {
+            try {
+                if (fs.existsSync(tmpDecryptedPath)) {
+                    fs.unlinkSync(tmpDecryptedPath);
+                }
+            }
+            catch {
+                // best-effort
+            }
+        }
+    };
+    try {
+        // ----- Step 5: Extract tarball ------------------------------------------
+        try {
+            await tarExtract({ file: tarPath, cwd: stagingDir });
+        }
+        catch (err) {
+            const msg = err instanceof Error ? err.message : String(err);
+            // Tar extraction failure is most likely due to corruption — treat as
+            // checksum mismatch (the corrupted bytes caused tar to fail before we
+            // could even read checksums).
+            throw new BundleError(72, 'E_CHECKSUM_MISMATCH', `Tar extraction failed: ${msg}`);
+        }
+        // ----- Step 6: Verify manifest.json exists -------------------------------
+        const manifestPath = path.join(stagingDir, 'manifest.json');
+        if (!fs.existsSync(manifestPath)) {
+            throw new BundleError(74, 'E_MANIFEST_MISSING', 'manifest.json is missing from the bundle.');
+        }
+        // ----- Step 7: Verify schemas/manifest-v1.json exists -------------------
+        const schemaPath = path.join(stagingDir, 'schemas', 'manifest-v1.json');
+        if (!fs.existsSync(schemaPath)) {
+            throw new BundleError(75, 'E_SCHEMAS_MISSING', 'schemas/manifest-v1.json is missing from the bundle.');
+        }
+        // ----- Step 8: Parse manifest.json ---------------------------------------
+        let manifest;
+        try {
+            manifest = JSON.parse(fs.readFileSync(manifestPath, 'utf-8'));
+        }
+        catch (err) {
+            const msg = err instanceof Error ? err.message : String(err);
+            throw new BundleError(71, 'E_BUNDLE_SCHEMA', `manifest.json is not valid JSON: ${msg}`);
+        }
+        // ----- Step 9: Validate manifest against bundled JSON Schema (Layer 3) --
+        const schemaErrors = validateAgainstJsonSchema(manifest, schemaPath);
+        if (schemaErrors.length > 0) {
+            throw new BundleError(71, 'E_BUNDLE_SCHEMA', `manifest.json failed schema validation: ${schemaErrors.join('; ')}`);
+        }
+        const manifestSchema = true;
+        // ----- Layer 2: Manifest self-hash verification --------------------------
+        // Per spec §4.1: compute SHA-256 of manifest JSON with integrity.manifestHash=""
+        // and compare to integrity.manifestHash.
+        if (manifest.integrity.manifestHash != null && manifest.integrity.manifestHash.length > 0) {
+            const manifestWithPlaceholder = {
+                ...manifest,
+                integrity: { ...manifest.integrity, manifestHash: '' },
+            };
+            const computedHash = sha256OfBuffer(Buffer.from(JSON.stringify(manifestWithPlaceholder), 'utf-8'));
+            if (computedHash !== manifest.integrity.manifestHash) {
+                throw new BundleError(71, 'E_BUNDLE_SCHEMA', 'Manifest self-hash mismatch — manifest.json may have been tampered with.');
+            }
+        }
+        // ----- Step 10: Checksum verification (Layer 4) --------------------------
+        const checksumsPath = path.join(stagingDir, 'checksums.sha256');
+        let checksums = true;
+        if (fs.existsSync(checksumsPath)) {
+            const checksumContent = fs.readFileSync(checksumsPath, 'utf-8');
+            const lines = checksumContent.split('\n').filter((l) => l.trim().length > 0);
+            for (const line of lines) {
+                // GNU sha256sum format: "<64 hex chars>  <relative path>"
+                const spaceIdx = line.indexOf('  ');
+                if (spaceIdx === -1)
+                    continue;
+                const expectedHash = line.slice(0, spaceIdx).trim();
+                const relPath = line.slice(spaceIdx + 2).trim();
+                const filePath = path.join(stagingDir, relPath);
+                if (!fs.existsSync(filePath)) {
+                    throw new BundleError(72, 'E_CHECKSUM_MISMATCH', `Checksummed file missing from staging: file=${relPath}`);
+                }
+                const actualHash = sha256OfFile(filePath);
+                if (actualHash !== expectedHash) {
+                    throw new BundleError(72, 'E_CHECKSUM_MISMATCH', `SHA-256 mismatch for file=${relPath}`);
+                }
+            }
+        }
+        else {
+            // checksums.sha256 missing from the extracted bundle is acceptable for
+            // bundles that were packed without checksums; pass through without failure.
+            checksums = true;
+        }
+        // ----- Step 11: SQLite integrity check (Layer 5) -------------------------
+        const sqliteIntegrity = true;
+        for (const dbEntry of manifest.databases) {
+            const dbPath = path.join(stagingDir, dbEntry.filename);
+            if (!fs.existsSync(dbPath))
+                continue;
+            let db = null;
+            try {
+                db = new DatabaseSync(dbPath, { readOnly: true });
+                const row = db.prepare('PRAGMA integrity_check').get();
+                if (row?.integrity_check !== 'ok') {
+                    throw new BundleError(73, 'E_SQLITE_INTEGRITY', `PRAGMA integrity_check failed for file=${dbEntry.filename}`);
+                }
+            }
+            catch (err) {
+                if (err instanceof BundleError)
+                    throw err;
+                throw new BundleError(73, 'E_SQLITE_INTEGRITY', `Could not open database for integrity check: file=${dbEntry.filename}`);
+            }
+            finally {
+                try {
+                    db?.close();
+                }
+                catch {
+                    // ignore
+                }
+            }
+        }
+        // ----- Step 12: Schema version compat warnings (Layer 6) ----------------
+        const warnings = [];
+        for (const dbEntry of manifest.databases) {
+            const warning = compareSchemaVersions(dbEntry.name, dbEntry.schemaVersion);
+            if (warning !== null) {
+                warnings.push(warning);
+            }
+        }
+        // ----- Step 13: Clean up temp decrypted file if any ----------------------
+        if (tmpDecryptedPath !== null) {
+            try {
+                if (fs.existsSync(tmpDecryptedPath)) {
+                    fs.unlinkSync(tmpDecryptedPath);
+                }
+            }
+            catch {
+                // best-effort
+            }
+        }
+        // ----- Return result -----------------------------------------------------
+        return {
+            stagingDir,
+            manifest,
+            verified: {
+                encryptionAuth,
+                manifestSchema,
+                checksums,
+                sqliteIntegrity,
+            },
+            warnings,
+        };
+    }
+    catch (err) {
+        cleanup();
+        throw err;
+    }
+}
+/**
+ * Remove the staging directory created by {@link unpackBundle}.
+ *
+ * Safe to call on a path that no longer exists (idempotent).
+ *
+ * @param stagingDir - Absolute path returned in {@link UnpackBundleResult.stagingDir}.
+ *
+ * @task T350
+ * @epic T311
+ */
+export function cleanupStaging(stagingDir) {
+    try {
+        fs.rmSync(stagingDir, { recursive: true, force: true });
+    }
+    catch {
+        // best-effort — do not throw on cleanup
+    }
+}
+//# sourceMappingURL=backup-unpack.js.map

package/dist/store/backup-unpack.js.map

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package/dist/store/backup.js

@@ -0,0 +1,94 @@
+/**
+ * Numbered backup system for CLEO data files.
+ * Maintains a rotating window of recent backups for rollback protection.
+ * @epic T4454
+ * @task T4457
+ */
+import { copyFile, rename as fsRename, mkdir, readdir, stat, unlink } from 'node:fs/promises';
+import { basename, join } from 'node:path';
+import { ExitCode } from '@cleocode/contracts';
+import { CleoError } from '../errors.js';
+const DEFAULT_MAX_BACKUPS = 5;
+/**
+ * Create a numbered backup of a file.
+ * Rotates existing backups (file.1 -> file.2, etc.) and removes excess.
+ */
+export async function createBackup(filePath, backupDir, maxBackups = DEFAULT_MAX_BACKUPS) {
+    try {
+        await mkdir(backupDir, { recursive: true });
+        const fileName = basename(filePath);
+        // Check if source file exists
+        try {
+            await stat(filePath);
+        }
+        catch {
+            throw new CleoError(ExitCode.FILE_ERROR, `Cannot backup: source file not found: ${filePath}`);
+        }
+        // Rotate existing backups (shift numbers up)
+        for (let i = maxBackups; i >= 1; i--) {
+            const current = join(backupDir, `${fileName}.${i}`);
+            if (i === maxBackups) {
+                // Remove oldest backup
+                try {
+                    await unlink(current);
+                }
+                catch {
+                    // File may not exist
+                }
+            }
+            else {
+                const next = join(backupDir, `${fileName}.${i + 1}`);
+                try {
+                    await stat(current);
+                    await fsRename(current, next);
+                }
+                catch {
+                    // File may not exist
+                }
+            }
+        }
+        // Create new backup as .1
+        const backupPath = join(backupDir, `${fileName}.1`);
+        await copyFile(filePath, backupPath);
+        return backupPath;
+    }
+    catch (err) {
+        if (err instanceof CleoError)
+            throw err;
+        throw new CleoError(ExitCode.FILE_ERROR, `Backup failed for: ${filePath}`, { cause: err });
+    }
+}
+/**
+ * List existing backups for a file, sorted by number (newest first).
+ */
+export async function listBackups(fileName, backupDir) {
+    try {
+        const entries = await readdir(backupDir);
+        const prefix = `${fileName}.`;
+        return entries
+            .filter((e) => e.startsWith(prefix) && /^\d+$/.test(e.slice(prefix.length)))
+            .sort((a, b) => {
+            const numA = parseInt(a.slice(prefix.length), 10);
+            const numB = parseInt(b.slice(prefix.length), 10);
+            return numA - numB;
+        })
+            .map((e) => join(backupDir, e));
+    }
+    catch {
+        return [];
+    }
+}
+/**
+ * Restore a file from its most recent backup.
+ * Returns the path of the backup that was restored.
+ */
+export async function restoreFromBackup(fileName, backupDir, targetPath) {
+    const backups = await listBackups(fileName, backupDir);
+    if (backups.length === 0) {
+        throw new CleoError(ExitCode.NOT_FOUND, `No backups found for: ${fileName}`);
+    }
+    const newest = backups[0];
+    await copyFile(newest, targetPath);
+    return newest;
+}
+//# sourceMappingURL=backup.js.map

package/dist/store/backup.js.map

@@ -0,0 +1 @@
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package/dist/store/brain-accessor.d.ts

@@ -71,10 +71,17 @@ export declare class BrainDataAccessor {
     getPageNode(id: string): Promise<BrainPageNodeRow | null>;
     findPageNodes(params?: {
         nodeType?: (typeof brainSchema.BRAIN_NODE_TYPES)[number];
+        minQualityScore?: number;
         limit?: number;
     }): Promise<BrainPageNodeRow[]>;
+    updatePageNode(id: string, updates: Partial<NewBrainPageNodeRow>): Promise<void>;
     removePageNode(id: string): Promise<void>;
     addPageEdge(edge: NewBrainPageEdgeRow): Promise<BrainPageEdgeRow>;
+    findPageEdges(params?: {
+        edgeType?: (typeof brainSchema.BRAIN_EDGE_TYPES)[number];
+        provenance?: string;
+        limit?: number;
+    }): Promise<BrainPageEdgeRow[]>;
     getPageEdges(nodeId: string, direction?: 'in' | 'out' | 'both'): Promise<BrainPageEdgeRow[]>;
     getNeighbors(nodeId: string, edgeType?: (typeof brainSchema.BRAIN_EDGE_TYPES)[number]): Promise<BrainPageNodeRow[]>;
     removePageEdge(fromId: string, toId: string, edgeType: (typeof brainSchema.BRAIN_EDGE_TYPES)[number]): Promise<void>;

package/dist/store/brain-accessor.d.ts.map

@@ -1 +1 @@
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