@cleocode/core 2026.3.76 → 2026.4.0

package/dist/store/atomic.js

@@ -0,0 +1,167 @@
+/**
+ * Atomic file write operations using write-file-atomic.
+ * Ensures writes are crash-safe: temp file -> validate -> rename.
+ * @epic T4454
+ * @task T4457
+ * @task T4721 - Added atomic database operations
+ */
+import { existsSync } from 'node:fs';
+import { mkdir, readFile, rename, unlink } from 'node:fs/promises';
+import { dirname } from 'node:path';
+import { ExitCode } from '@cleocode/contracts';
+import writeFileAtomic from 'write-file-atomic';
+import { CleoError } from '../errors.js';
+/**
+ * Write data to a file atomically.
+ * Creates parent directories if they don't exist.
+ * Uses write-file-atomic for crash-safe writes (temp file -> rename).
+ */
+export async function atomicWrite(filePath, data, options) {
+    try {
+        await mkdir(dirname(filePath), { recursive: true });
+        await writeFileAtomic(filePath, data, {
+            encoding: options?.encoding ?? 'utf8',
+            mode: options?.mode,
+        });
+    }
+    catch (err) {
+        throw new CleoError(ExitCode.FILE_ERROR, `Atomic write failed: ${filePath}`, { cause: err });
+    }
+}
+/**
+ * Read a file and return its contents.
+ * Returns null if the file does not exist.
+ */
+export async function safeReadFile(filePath) {
+    try {
+        return await readFile(filePath, 'utf8');
+    }
+    catch (err) {
+        if (err instanceof Error && 'code' in err && err.code === 'ENOENT') {
+            return null;
+        }
+        throw new CleoError(ExitCode.FILE_ERROR, `Failed to read: ${filePath}`, { cause: err });
+    }
+}
+/**
+ * Write JSON data atomically with consistent formatting.
+ */
+export async function atomicWriteJson(filePath, data, options) {
+    const json = JSON.stringify(data, null, options?.indent ?? 2) + '\n';
+    await atomicWrite(filePath, json);
+}
+/**
+ * Perform atomic database migration using rename operations.
+ *
+ * Pattern:
+ *   1. Write new database to temp file (tasks.db.new)
+ *   2. Validate temp database integrity
+ *   3. Rename existing tasks.db → tasks.db.backup
+ *   4. Rename temp → tasks.db (atomic)
+ *   5. Only delete backup on success
+ *
+ * @param dbPath - Path to the database file (e.g., tasks.db)
+ * @param tempPath - Path to temporary database (e.g., tasks.db.new)
+ * @param validateFn - Async function to validate the temp database
+ * @returns Result with paths and success status
+ */
+export async function atomicDatabaseMigration(dbPath, tempPath, validateFn) {
+    const backupPath = `${dbPath}.backup`;
+    try {
+        // Step 1: Validate temp database exists
+        if (!existsSync(tempPath)) {
+            throw new Error(`Temp database not found: ${tempPath}`);
+        }
+        // Step 2: Validate the temp database integrity
+        const isValid = await validateFn(tempPath);
+        if (!isValid) {
+            throw new Error(`Temp database validation failed: ${tempPath}`);
+        }
+        // Step 3: If existing database exists, rename to backup
+        if (existsSync(dbPath)) {
+            await rename(dbPath, backupPath);
+        }
+        // Step 4: Atomically rename temp to final (atomic on POSIX systems)
+        await rename(tempPath, dbPath);
+        return {
+            success: true,
+            tempPath,
+            backupPath: existsSync(backupPath) ? backupPath : undefined,
+        };
+    }
+    catch (err) {
+        return {
+            success: false,
+            tempPath,
+            backupPath: existsSync(backupPath) ? backupPath : undefined,
+            error: String(err),
+        };
+    }
+}
+/**
+ * Restore database from backup after failed migration.
+ *
+ * @param dbPath - Path to the database file
+ * @param backupPath - Path to the backup file
+ * @returns true if restore succeeded
+ */
+export async function restoreDatabaseFromBackup(dbPath, backupPath) {
+    try {
+        if (!existsSync(backupPath)) {
+            return false;
+        }
+        // If a partial database exists, remove it
+        if (existsSync(dbPath)) {
+            await unlink(dbPath);
+        }
+        // Restore from backup
+        await rename(backupPath, dbPath);
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Clean up migration artifacts after successful migration.
+ *
+ * @param backupPath - Path to backup file to delete
+ * @returns true if cleanup succeeded
+ */
+export async function cleanupMigrationArtifacts(backupPath) {
+    try {
+        if (existsSync(backupPath)) {
+            await unlink(backupPath);
+        }
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Validate SQLite database integrity by attempting to open it.
+ *
+ * @param dbPath - Path to database file
+ * @returns true if database is valid
+ */
+export async function validateSqliteDatabase(dbPath) {
+    try {
+        const { createRequire } = await import('node:module');
+        const _req = createRequire(import.meta.url);
+        const { DatabaseSync } = _req('node:sqlite');
+        const db = new DatabaseSync(dbPath, { readOnly: true });
+        const integrityRow = db.prepare('PRAGMA integrity_check').get();
+        const isOk = integrityRow?.integrity_check === 'ok';
+        const tableRow = db
+            .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name='tasks'")
+            .get();
+        const hasTasksTable = !!tableRow;
+        db.close();
+        return isOk && hasTasksTable;
+    }
+    catch {
+        return false;
+    }
+}
+//# sourceMappingURL=atomic.js.map

package/dist/store/atomic.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

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package/dist/store/brain-accessor.js

@@ -0,0 +1,397 @@
+/**
+ * Data accessor for brain.db — CRUD operations for decisions, patterns,
+ * learnings, and memory links.
+ *
+ * Wraps drizzle ORM queries over the brain.db singleton. All methods are
+ * async (sqlite-proxy) and return typed rows from brain-schema.ts.
+ *
+ * @epic T5149
+ * @task T5128
+ */
+import { and, asc, desc, eq, gte, or } from 'drizzle-orm';
+import * as brainSchema from './brain-schema.js';
+import { getBrainDb } from './brain-sqlite.js';
+export class BrainDataAccessor {
+    db;
+    constructor(db) {
+        this.db = db;
+    }
+    // =========================================================================
+    // Decisions CRUD
+    // =========================================================================
+    async addDecision(row) {
+        await this.db.insert(brainSchema.brainDecisions).values(row);
+        const result = await this.db
+            .select()
+            .from(brainSchema.brainDecisions)
+            .where(eq(brainSchema.brainDecisions.id, row.id));
+        return result[0];
+    }
+    async getDecision(id) {
+        const result = await this.db
+            .select()
+            .from(brainSchema.brainDecisions)
+            .where(eq(brainSchema.brainDecisions.id, id));
+        return result[0] ?? null;
+    }
+    async findDecisions(params = {}) {
+        const conditions = [];
+        if (params.type) {
+            conditions.push(eq(brainSchema.brainDecisions.type, params.type));
+        }
+        if (params.confidence) {
+            conditions.push(eq(brainSchema.brainDecisions.confidence, params.confidence));
+        }
+        if (params.outcome) {
+            conditions.push(eq(brainSchema.brainDecisions.outcome, params.outcome));
+        }
+        if (params.contextTaskId) {
+            conditions.push(eq(brainSchema.brainDecisions.contextTaskId, params.contextTaskId));
+        }
+        let query = this.db
+            .select()
+            .from(brainSchema.brainDecisions)
+            .orderBy(desc(brainSchema.brainDecisions.createdAt));
+        if (conditions.length > 0) {
+            query = query.where(and(...conditions));
+        }
+        if (params.limit) {
+            query = query.limit(params.limit);
+        }
+        return query;
+    }
+    async updateDecision(id, updates) {
+        await this.db
+            .update(brainSchema.brainDecisions)
+            .set({ ...updates, updatedAt: new Date().toISOString().replace('T', ' ').slice(0, 19) })
+            .where(eq(brainSchema.brainDecisions.id, id));
+    }
+    // =========================================================================
+    // Patterns CRUD
+    // =========================================================================
+    async addPattern(row) {
+        await this.db.insert(brainSchema.brainPatterns).values(row);
+        const result = await this.db
+            .select()
+            .from(brainSchema.brainPatterns)
+            .where(eq(brainSchema.brainPatterns.id, row.id));
+        return result[0];
+    }
+    async getPattern(id) {
+        const result = await this.db
+            .select()
+            .from(brainSchema.brainPatterns)
+            .where(eq(brainSchema.brainPatterns.id, id));
+        return result[0] ?? null;
+    }
+    async findPatterns(params = {}) {
+        const conditions = [];
+        if (params.type) {
+            conditions.push(eq(brainSchema.brainPatterns.type, params.type));
+        }
+        if (params.impact) {
+            conditions.push(eq(brainSchema.brainPatterns.impact, params.impact));
+        }
+        if (params.minFrequency !== undefined) {
+            conditions.push(gte(brainSchema.brainPatterns.frequency, params.minFrequency));
+        }
+        let query = this.db
+            .select()
+            .from(brainSchema.brainPatterns)
+            .orderBy(desc(brainSchema.brainPatterns.frequency));
+        if (conditions.length > 0) {
+            query = query.where(and(...conditions));
+        }
+        if (params.limit) {
+            query = query.limit(params.limit);
+        }
+        return query;
+    }
+    async updatePattern(id, updates) {
+        await this.db
+            .update(brainSchema.brainPatterns)
+            .set({ ...updates, updatedAt: new Date().toISOString().replace('T', ' ').slice(0, 19) })
+            .where(eq(brainSchema.brainPatterns.id, id));
+    }
+    // =========================================================================
+    // Learnings CRUD
+    // =========================================================================
+    async addLearning(row) {
+        await this.db.insert(brainSchema.brainLearnings).values(row);
+        const result = await this.db
+            .select()
+            .from(brainSchema.brainLearnings)
+            .where(eq(brainSchema.brainLearnings.id, row.id));
+        return result[0];
+    }
+    async getLearning(id) {
+        const result = await this.db
+            .select()
+            .from(brainSchema.brainLearnings)
+            .where(eq(brainSchema.brainLearnings.id, id));
+        return result[0] ?? null;
+    }
+    async findLearnings(params = {}) {
+        const conditions = [];
+        if (params.minConfidence !== undefined) {
+            conditions.push(gte(brainSchema.brainLearnings.confidence, params.minConfidence));
+        }
+        if (params.actionable !== undefined) {
+            conditions.push(eq(brainSchema.brainLearnings.actionable, params.actionable));
+        }
+        let query = this.db
+            .select()
+            .from(brainSchema.brainLearnings)
+            .orderBy(desc(brainSchema.brainLearnings.confidence));
+        if (conditions.length > 0) {
+            query = query.where(and(...conditions));
+        }
+        if (params.limit) {
+            query = query.limit(params.limit);
+        }
+        return query;
+    }
+    async updateLearning(id, updates) {
+        await this.db
+            .update(brainSchema.brainLearnings)
+            .set({ ...updates, updatedAt: new Date().toISOString().replace('T', ' ').slice(0, 19) })
+            .where(eq(brainSchema.brainLearnings.id, id));
+    }
+    // =========================================================================
+    // Observations CRUD
+    // =========================================================================
+    async addObservation(row) {
+        await this.db.insert(brainSchema.brainObservations).values(row);
+        const result = await this.db
+            .select()
+            .from(brainSchema.brainObservations)
+            .where(eq(brainSchema.brainObservations.id, row.id));
+        return result[0];
+    }
+    async getObservation(id) {
+        const result = await this.db
+            .select()
+            .from(brainSchema.brainObservations)
+            .where(eq(brainSchema.brainObservations.id, id));
+        return result[0] ?? null;
+    }
+    async findObservations(params = {}) {
+        const conditions = [];
+        if (params.type) {
+            conditions.push(eq(brainSchema.brainObservations.type, params.type));
+        }
+        if (params.project) {
+            conditions.push(eq(brainSchema.brainObservations.project, params.project));
+        }
+        if (params.sourceType) {
+            conditions.push(eq(brainSchema.brainObservations.sourceType, params.sourceType));
+        }
+        if (params.sourceSessionId) {
+            conditions.push(eq(brainSchema.brainObservations.sourceSessionId, params.sourceSessionId));
+        }
+        let query = this.db
+            .select()
+            .from(brainSchema.brainObservations)
+            .orderBy(desc(brainSchema.brainObservations.createdAt));
+        if (conditions.length > 0) {
+            query = query.where(and(...conditions));
+        }
+        if (params.limit) {
+            query = query.limit(params.limit);
+        }
+        return query;
+    }
+    async updateObservation(id, updates) {
+        await this.db
+            .update(brainSchema.brainObservations)
+            .set({ ...updates, updatedAt: new Date().toISOString().replace('T', ' ').slice(0, 19) })
+            .where(eq(brainSchema.brainObservations.id, id));
+    }
+    // =========================================================================
+    // Memory Links CRUD
+    // =========================================================================
+    async addLink(row) {
+        await this.db.insert(brainSchema.brainMemoryLinks).values(row);
+    }
+    async getLinksForMemory(memoryType, memoryId) {
+        return this.db
+            .select()
+            .from(brainSchema.brainMemoryLinks)
+            .where(and(eq(brainSchema.brainMemoryLinks.memoryType, memoryType), eq(brainSchema.brainMemoryLinks.memoryId, memoryId)))
+            .orderBy(asc(brainSchema.brainMemoryLinks.createdAt));
+    }
+    async getLinksForTask(taskId) {
+        return this.db
+            .select()
+            .from(brainSchema.brainMemoryLinks)
+            .where(eq(brainSchema.brainMemoryLinks.taskId, taskId))
+            .orderBy(asc(brainSchema.brainMemoryLinks.createdAt));
+    }
+    async removeLink(memoryType, memoryId, taskId, linkType) {
+        await this.db
+            .delete(brainSchema.brainMemoryLinks)
+            .where(and(eq(brainSchema.brainMemoryLinks.memoryType, memoryType), eq(brainSchema.brainMemoryLinks.memoryId, memoryId), eq(brainSchema.brainMemoryLinks.taskId, taskId), eq(brainSchema.brainMemoryLinks.linkType, linkType)));
+    }
+    // =========================================================================
+    // Sticky Notes CRUD
+    // =========================================================================
+    async addStickyNote(row) {
+        await this.db.insert(brainSchema.brainStickyNotes).values(row);
+        const result = await this.db
+            .select()
+            .from(brainSchema.brainStickyNotes)
+            .where(eq(brainSchema.brainStickyNotes.id, row.id));
+        return result[0];
+    }
+    async getStickyNote(id) {
+        const result = await this.db
+            .select()
+            .from(brainSchema.brainStickyNotes)
+            .where(eq(brainSchema.brainStickyNotes.id, id));
+        return result[0] ?? null;
+    }
+    async findStickyNotes(params = {}) {
+        const conditions = [];
+        if (params.status) {
+            conditions.push(eq(brainSchema.brainStickyNotes.status, params.status));
+        }
+        if (params.color) {
+            conditions.push(eq(brainSchema.brainStickyNotes.color, params.color));
+        }
+        if (params.priority) {
+            conditions.push(eq(brainSchema.brainStickyNotes.priority, params.priority));
+        }
+        let query = this.db
+            .select()
+            .from(brainSchema.brainStickyNotes)
+            .orderBy(desc(brainSchema.brainStickyNotes.createdAt));
+        if (conditions.length > 0) {
+            query = query.where(and(...conditions));
+        }
+        if (params.limit) {
+            query = query.limit(params.limit);
+        }
+        return query;
+    }
+    async updateStickyNote(id, updates) {
+        await this.db
+            .update(brainSchema.brainStickyNotes)
+            .set({ ...updates, updatedAt: new Date().toISOString().replace('T', ' ').slice(0, 19) })
+            .where(eq(brainSchema.brainStickyNotes.id, id));
+    }
+    async deleteStickyNote(id) {
+        await this.db
+            .delete(brainSchema.brainStickyNotes)
+            .where(eq(brainSchema.brainStickyNotes.id, id));
+    }
+    // =========================================================================
+    // PageIndex Node CRUD (T5383)
+    // =========================================================================
+    async addPageNode(node) {
+        await this.db.insert(brainSchema.brainPageNodes).values(node);
+        const result = await this.db
+            .select()
+            .from(brainSchema.brainPageNodes)
+            .where(eq(brainSchema.brainPageNodes.id, node.id));
+        return result[0];
+    }
+    async getPageNode(id) {
+        const result = await this.db
+            .select()
+            .from(brainSchema.brainPageNodes)
+            .where(eq(brainSchema.brainPageNodes.id, id));
+        return result[0] ?? null;
+    }
+    async findPageNodes(params = {}) {
+        const conditions = [];
+        if (params.nodeType) {
+            conditions.push(eq(brainSchema.brainPageNodes.nodeType, params.nodeType));
+        }
+        let query = this.db
+            .select()
+            .from(brainSchema.brainPageNodes)
+            .orderBy(desc(brainSchema.brainPageNodes.createdAt));
+        if (conditions.length > 0) {
+            query = query.where(and(...conditions));
+        }
+        if (params.limit) {
+            query = query.limit(params.limit);
+        }
+        return query;
+    }
+    async removePageNode(id) {
+        // Remove associated edges first (both directions)
+        await this.db
+            .delete(brainSchema.brainPageEdges)
+            .where(or(eq(brainSchema.brainPageEdges.fromId, id), eq(brainSchema.brainPageEdges.toId, id)));
+        // Remove the node
+        await this.db.delete(brainSchema.brainPageNodes).where(eq(brainSchema.brainPageNodes.id, id));
+    }
+    // =========================================================================
+    // PageIndex Edge CRUD (T5383)
+    // =========================================================================
+    async addPageEdge(edge) {
+        await this.db.insert(brainSchema.brainPageEdges).values(edge);
+        const result = await this.db
+            .select()
+            .from(brainSchema.brainPageEdges)
+            .where(and(eq(brainSchema.brainPageEdges.fromId, edge.fromId), eq(brainSchema.brainPageEdges.toId, edge.toId), eq(brainSchema.brainPageEdges.edgeType, edge.edgeType)));
+        return result[0];
+    }
+    async getPageEdges(nodeId, direction = 'both') {
+        if (direction === 'out') {
+            return this.db
+                .select()
+                .from(brainSchema.brainPageEdges)
+                .where(eq(brainSchema.brainPageEdges.fromId, nodeId))
+                .orderBy(asc(brainSchema.brainPageEdges.createdAt));
+        }
+        if (direction === 'in') {
+            return this.db
+                .select()
+                .from(brainSchema.brainPageEdges)
+                .where(eq(brainSchema.brainPageEdges.toId, nodeId))
+                .orderBy(asc(brainSchema.brainPageEdges.createdAt));
+        }
+        // both
+        return this.db
+            .select()
+            .from(brainSchema.brainPageEdges)
+            .where(or(eq(brainSchema.brainPageEdges.fromId, nodeId), eq(brainSchema.brainPageEdges.toId, nodeId)))
+            .orderBy(asc(brainSchema.brainPageEdges.createdAt));
+    }
+    async getNeighbors(nodeId, edgeType) {
+        // Get edges from this node
+        const conditions = [eq(brainSchema.brainPageEdges.fromId, nodeId)];
+        if (edgeType) {
+            conditions.push(eq(brainSchema.brainPageEdges.edgeType, edgeType));
+        }
+        const edges = await this.db
+            .select()
+            .from(brainSchema.brainPageEdges)
+            .where(and(...conditions));
+        if (edges.length === 0)
+            return [];
+        const neighborIds = edges.map((e) => e.toId);
+        const nodes = [];
+        for (const nid of neighborIds) {
+            const node = await this.getPageNode(nid);
+            if (node)
+                nodes.push(node);
+        }
+        return nodes;
+    }
+    async removePageEdge(fromId, toId, edgeType) {
+        await this.db
+            .delete(brainSchema.brainPageEdges)
+            .where(and(eq(brainSchema.brainPageEdges.fromId, fromId), eq(brainSchema.brainPageEdges.toId, toId), eq(brainSchema.brainPageEdges.edgeType, edgeType)));
+    }
+}
+/**
+ * Factory: get a BrainDataAccessor backed by the brain.db singleton.
+ */
+export async function getBrainAccessor(cwd) {
+    const db = await getBrainDb(cwd);
+    return new BrainDataAccessor(db);
+}
+//# sourceMappingURL=brain-accessor.js.map