@cleocode/core 2026.4.9 → 2026.4.11

package/dist/store/import-sort.js

@@ -0,0 +1,121 @@
+/**
+ * Topological sort for import order using Kahn's algorithm.
+ * Ported from lib/data/import-sort.sh
+ *
+ * Ensures tasks are imported in dependency order where:
+ * 1. Parents are imported before children (parentId references)
+ * 2. Dependencies are imported before dependents (depends[] references)
+ *
+ * @task T4552
+ * @epic T4545
+ */
+import { ExitCode } from '@cleocode/contracts';
+import { CleoError } from '../errors.js';
+/**
+ * Topological sort for task import order using Kahn's algorithm.
+ *
+ * Ensures tasks are imported in dependency order:
+ * - Parents before children (parentId references)
+ * - Dependencies before dependents (depends[] references)
+ * - Only counts edges to tasks within the set (external deps ignored)
+ *
+ * @task T4552
+ */
+export function topologicalSortTasks(tasks) {
+    if (tasks.length === 0)
+        return [];
+    // Build lookup from id to index
+    const idToIndex = new Map();
+    for (let i = 0; i < tasks.length; i++) {
+        idToIndex.set(tasks[i].id, i);
+    }
+    // Initialize graph nodes
+    const nodes = tasks.map((task) => {
+        // Count in-degree: edges from parentId + depends that are within the set
+        let inDegree = 0;
+        if (task.parentId && idToIndex.has(task.parentId)) {
+            inDegree++;
+        }
+        const deps = task.depends ?? [];
+        for (const dep of deps) {
+            if (idToIndex.has(dep)) {
+                inDegree++;
+            }
+        }
+        return {
+            id: task.id,
+            inDegree,
+            children: [],
+            dependents: [],
+        };
+    });
+    // Build reverse edges (parent -> children, dep -> dependents)
+    for (const task of tasks) {
+        // Add to parent's children list
+        if (task.parentId) {
+            const parentIdx = idToIndex.get(task.parentId);
+            if (parentIdx !== undefined) {
+                nodes[parentIdx].children.push(task.id);
+            }
+        }
+        // Add to each dep's dependents list
+        const deps = task.depends ?? [];
+        for (const dep of deps) {
+            const depIdx = idToIndex.get(dep);
+            if (depIdx !== undefined) {
+                nodes[depIdx].dependents.push(task.id);
+            }
+        }
+    }
+    // Build node lookup by ID for efficient access
+    const nodeById = new Map();
+    for (const node of nodes) {
+        nodeById.set(node.id, node);
+    }
+    // Kahn's algorithm: initialize queue with zero in-degree nodes
+    const queue = [];
+    for (const node of nodes) {
+        if (node.inDegree === 0) {
+            queue.push(node.id);
+        }
+    }
+    const result = [];
+    while (queue.length > 0) {
+        const current = queue.shift();
+        result.push(current);
+        const currentNode = nodeById.get(current);
+        // Process all successors (children + dependents)
+        const successors = [...currentNode.children, ...currentNode.dependents];
+        for (const successorId of successors) {
+            const successor = nodeById.get(successorId);
+            if (!successor)
+                continue;
+            successor.inDegree--;
+            if (successor.inDegree === 0) {
+                queue.push(successorId);
+            }
+        }
+    }
+    // Cycle detection
+    if (result.length !== tasks.length) {
+        const processed = new Set(result);
+        const unprocessed = tasks.map((t) => t.id).filter((id) => !processed.has(id));
+        throw new CleoError(ExitCode.VALIDATION_ERROR, `Cycle detected in task dependencies. Tasks in cycle: ${unprocessed.join(', ')}`);
+    }
+    return result;
+}
+/**
+ * Detect cycles in task dependency graph.
+ * Returns true if no cycles, false if cycles detected.
+ * @task T4552
+ */
+export function detectCycles(tasks) {
+    try {
+        topologicalSortTasks(tasks);
+        return true; // No cycles
+    }
+    catch {
+        return false; // Cycles detected
+    }
+}
+//# sourceMappingURL=import-sort.js.map

package/dist/store/import-sort.js.map

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package/dist/store/index.d.ts

@@ -17,6 +17,7 @@ export { acquireLock, isLocked, withLock } from './lock.js';
 export type { AddTaskOptions, AddTaskResult, AnalysisResult, ArchiveTasksOptions, ArchiveTasksResult, CompleteTaskOptions, CompleteTaskResult, DeleteTaskOptions, DeleteTaskResult, FindTasksOptions, FindTasksResult, ListTasksOptions, ListTasksResult, SessionFilters, StoreEngine, StoreProvider, TaskCurrentResult, TaskFilters, TaskStartResult, TaskWorkHistoryEntry, UpdateTaskOptions, UpdateTaskResult, } from './provider.js';
 export { createStoreProvider } from './provider.js';
 export { getSafetyStatus, isSafetyEnabled, SafetyDataAccessor, wrapWithSafety, } from './safety-data-accessor.js';
+export { listBrainBackups, listSqliteBackups, listSqliteBackupsAll, vacuumIntoBackup, vacuumIntoBackupAll, } from './sqlite-backup.js';
 /**
  * Get a StoreProvider instance for the given working directory.
  * Convenience wrapper around createStoreProvider with auto-detection.

package/dist/store/index.d.ts.map

@@ -1 +1 @@
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package/dist/store/index.js

@@ -0,0 +1,29 @@
+/**
+ * Unified store interface for CLEO V2 data access.
+ * @epic T4454
+ * @task T4457
+ * @task T4645
+ * @task T4745
+ */
+export { atomicWrite, atomicWriteJson, safeReadFile } from './atomic.js';
+export { createBackup, listBackups, restoreFromBackup } from './backup.js';
+export { forceCheckpointBeforeOperation } from './data-safety.js';
+export { DataSafetyError, disableSafety, enableSafety, forceSafetyCheckpoint, getSafetyStats, resetSafetyStats, runDataIntegrityCheck, } from './data-safety-central.js';
+export { appendJsonl, computeChecksum, readJson, readJsonRequired, saveJson, } from './json.js';
+export { acquireLock, isLocked, withLock } from './lock.js';
+export { createStoreProvider } from './provider.js';
+// Safety-enabled DataAccessor exports (@task T4745)
+export { getSafetyStatus, isSafetyEnabled, SafetyDataAccessor, wrapWithSafety, } from './safety-data-accessor.js';
+export { listBrainBackups, listSqliteBackups, listSqliteBackupsAll, vacuumIntoBackup, vacuumIntoBackupAll, } from './sqlite-backup.js';
+/**
+ * Get a StoreProvider instance for the given working directory.
+ * Convenience wrapper around createStoreProvider with auto-detection.
+ *
+ * @task T4645
+ * @epic T4638
+ */
+export async function getStore(cwd) {
+    const { createStoreProvider: create } = await import('./provider.js');
+    return create(undefined, cwd);
+}
+//# sourceMappingURL=index.js.map

package/dist/store/index.js.map

@@ -0,0 +1 @@
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package/dist/store/json.js

@@ -0,0 +1,208 @@
+/**
+ * JSON read/write with schema validation, locking, and backup.
+ * This is the primary data access layer for CLEO data files.
+ * @epic T4454
+ * @task T4457
+ */
+import { createHash } from 'node:crypto';
+import { ExitCode } from '@cleocode/contracts';
+import { CleoError } from '../errors.js';
+import { atomicWrite, atomicWriteJson, safeReadFile } from './atomic.js';
+import { createBackup } from './backup.js';
+import { withLock } from './lock.js';
+/**
+ * Read and parse a JSON file.
+ * Returns null if the file does not exist.
+ */
+export async function readJson(filePath) {
+    const content = await safeReadFile(filePath);
+    if (content === null)
+        return null;
+    try {
+        return JSON.parse(content);
+    }
+    catch (err) {
+        throw new CleoError(ExitCode.VALIDATION_ERROR, `Invalid JSON in: ${filePath}`, { cause: err });
+    }
+}
+/**
+ * Read a JSON file, throwing if it doesn't exist.
+ */
+export async function readJsonRequired(filePath) {
+    const data = await readJson(filePath);
+    if (data === null) {
+        throw new CleoError(ExitCode.NOT_FOUND, `Required file not found: ${filePath}`);
+    }
+    return data;
+}
+/**
+ * Compute a truncated SHA-256 checksum of a value.
+ * Used for integrity verification (matches Bash CLI's 16-char hex format).
+ */
+export function computeChecksum(data) {
+    const json = JSON.stringify(data);
+    const hash = createHash('sha256').update(json).digest('hex');
+    return hash.substring(0, 16);
+}
+/**
+ * Save JSON data with optional locking, backup, and validation.
+ * Follows the CLEO atomic write pattern:
+ *   1. Acquire lock
+ *   2. Validate data
+ *   3. Create backup of existing file
+ *   4. Atomic write (temp file -> rename)
+ *   5. Release lock
+ */
+export async function saveJson(filePath, data, options) {
+    await withLock(filePath, async () => {
+        // Validate before write
+        if (options?.validate) {
+            try {
+                await options.validate(data);
+            }
+            catch (err) {
+                throw new CleoError(ExitCode.VALIDATION_ERROR, `Validation failed before write: ${filePath}`, { cause: err });
+            }
+        }
+        // Create backup if configured
+        if (options?.backupDir) {
+            try {
+                await createBackup(filePath, options.backupDir, options.maxBackups);
+            }
+            catch {
+                // Backup failure is non-fatal for first write (file may not exist yet)
+            }
+        }
+        // Atomic write
+        await atomicWriteJson(filePath, data, { indent: options?.indent });
+        // Dispatch Notification hook (best-effort, fire-and-forget)
+        import('../hooks/registry.js')
+            .then(({ hooks: h }) => h.dispatch('Notification', process.cwd(), {
+            timestamp: new Date().toISOString(),
+            filePath,
+            changeType: 'write',
+        }))
+            .catch(() => {
+            /* hook errors are non-fatal */
+        });
+    });
+}
+/**
+ * Append a line to a JSONL file atomically.
+ * Used for manifest entries and audit logs.
+ */
+export async function appendJsonl(filePath, entry) {
+    const existing = await safeReadFile(filePath);
+    const line = JSON.stringify(entry);
+    const content = existing ? existing.trimEnd() + '\n' + line + '\n' : line + '\n';
+    await atomicWrite(filePath, content);
+}
+/**
+ * Read log entries from a hybrid JSON/JSONL file.
+ * Handles three formats:
+ *   1. Pure JSON: `{ "entries": [...] }` (legacy bash format)
+ *   2. Pure JSONL: one JSON object per line (new TS format)
+ *   3. Hybrid: JSON object followed by JSONL lines (migration state)
+ * Returns a flat array of all entries found.
+ * @task T4622
+ */
+export async function readLogEntries(filePath) {
+    const content = await safeReadFile(filePath);
+    if (content === null)
+        return [];
+    const trimmed = content.trim();
+    if (!trimmed)
+        return [];
+    // Fast path: try parsing as a single JSON object
+    try {
+        const parsed = JSON.parse(trimmed);
+        if (Array.isArray(parsed))
+            return parsed;
+        if (parsed && typeof parsed === 'object' && Array.isArray(parsed.entries)) {
+            return parsed.entries;
+        }
+        // Single object, wrap in array
+        return [parsed];
+    }
+    catch {
+        // Not valid JSON - handle hybrid format
+    }
+    // Hybrid format: find where the initial JSON object ends, then parse JSONL after it
+    const entries = [];
+    if (trimmed.startsWith('{')) {
+        // Find the matching closing brace for the initial JSON object
+        let depth = 0;
+        let inString = false;
+        let escaped = false;
+        let jsonEnd = -1;
+        for (let i = 0; i < trimmed.length; i++) {
+            const ch = trimmed[i];
+            if (escaped) {
+                escaped = false;
+                continue;
+            }
+            if (ch === '\\' && inString) {
+                escaped = true;
+                continue;
+            }
+            if (ch === '"') {
+                inString = !inString;
+                continue;
+            }
+            if (inString)
+                continue;
+            if (ch === '{')
+                depth++;
+            else if (ch === '}') {
+                depth--;
+                if (depth === 0) {
+                    jsonEnd = i + 1;
+                    break;
+                }
+            }
+        }
+        if (jsonEnd > 0) {
+            // Parse the initial JSON object
+            try {
+                const initialJson = JSON.parse(trimmed.substring(0, jsonEnd));
+                if (initialJson && Array.isArray(initialJson.entries)) {
+                    entries.push(...initialJson.entries);
+                }
+            }
+            catch {
+                // Corrupted initial JSON - skip it
+            }
+            // Parse remaining lines as JSONL
+            const remainder = trimmed.substring(jsonEnd).trim();
+            if (remainder) {
+                for (const line of remainder.split('\n')) {
+                    const l = line.trim();
+                    if (!l || !l.startsWith('{'))
+                        continue;
+                    try {
+                        entries.push(JSON.parse(l));
+                    }
+                    catch {
+                        // Skip unparseable lines
+                    }
+                }
+            }
+        }
+    }
+    else {
+        // Pure JSONL (no initial JSON object)
+        for (const line of trimmed.split('\n')) {
+            const l = line.trim();
+            if (!l || !l.startsWith('{'))
+                continue;
+            try {
+                entries.push(JSON.parse(l));
+            }
+            catch {
+                // Skip unparseable lines
+            }
+        }
+    }
+    return entries;
+}
+//# sourceMappingURL=json.js.map

package/dist/store/json.js.map

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package/dist/store/lifecycle-store.js

@@ -0,0 +1,249 @@
+/**
+ * SQLite-backed lifecycle store operations.
+ *
+ * Query and mutation functions for lifecycle pipeline tables:
+ * lifecycle_pipelines, lifecycle_stages, lifecycle_gate_results,
+ * lifecycle_evidence, lifecycle_transitions.
+ *
+ * Used by src/core/lifecycle/resume.ts to avoid direct store-layer imports.
+ *
+ * @task T4832
+ * @epic T4454
+ */
+import { and, asc, desc, eq, inArray, sql } from 'drizzle-orm';
+import { getDb } from './sqlite.js';
+import * as schema from './tasks-schema.js';
+// =============================================================================
+// PIPELINE QUERIES
+// =============================================================================
+/**
+ * Find active pipelines joined with their stages and tasks.
+ * Optionally filters by specific task IDs.
+ *
+ * @param taskIds - Optional list of task IDs to filter by
+ * @param cwd - Working directory for database
+ * @returns Rows with pipeline, stage, and task data
+ */
+export async function findActivePipelinesWithStagesAndTasks(taskIds, cwd) {
+    const db = await getDb(cwd);
+    const conditions = [eq(schema.lifecyclePipelines.status, 'active')];
+    if (taskIds && taskIds.length > 0) {
+        conditions.push(inArray(schema.lifecyclePipelines.taskId, taskIds));
+    }
+    return db
+        .select({
+        pipeline: schema.lifecyclePipelines,
+        stage: schema.lifecycleStages,
+        task: schema.tasks,
+    })
+        .from(schema.lifecyclePipelines)
+        .innerJoin(schema.lifecycleStages, eq(schema.lifecycleStages.pipelineId, schema.lifecyclePipelines.id))
+        .innerJoin(schema.tasks, eq(schema.tasks.id, schema.lifecyclePipelines.taskId))
+        .where(and(...conditions))
+        .orderBy(asc(schema.tasks.priority), desc(schema.lifecyclePipelines.startedAt))
+        .all();
+}
+/**
+ * Find a pipeline with its current stage and task by taskId.
+ * Matches stages where stageName equals the pipeline's currentStageId.
+ *
+ * @param taskId - Task ID to look up
+ * @param cwd - Working directory for database
+ * @returns Matching rows (typically 0 or 1)
+ */
+export async function findPipelineWithCurrentStageAndTask(taskId, cwd) {
+    const db = await getDb(cwd);
+    return db
+        .select({
+        pipeline: schema.lifecyclePipelines,
+        stage: schema.lifecycleStages,
+        task: schema.tasks,
+    })
+        .from(schema.lifecyclePipelines)
+        .innerJoin(schema.lifecycleStages, eq(schema.lifecycleStages.pipelineId, schema.lifecyclePipelines.id))
+        .innerJoin(schema.tasks, eq(schema.tasks.id, schema.lifecyclePipelines.taskId))
+        .where(and(eq(schema.lifecyclePipelines.taskId, taskId), eq(schema.lifecycleStages.stageName, sql `${schema.lifecyclePipelines.currentStageId}`)))
+        .limit(1)
+        .all();
+}
+/**
+ * Find a pipeline and a specific stage by taskId and stageName.
+ *
+ * @param taskId - Task ID
+ * @param stageName - Stage name to match
+ * @param cwd - Working directory for database
+ * @returns Matching rows (typically 0 or 1)
+ */
+export async function findPipelineWithStage(taskId, stageName, cwd) {
+    const db = await getDb(cwd);
+    return db
+        .select({
+        pipeline: schema.lifecyclePipelines,
+        stageRecord: schema.lifecycleStages,
+    })
+        .from(schema.lifecyclePipelines)
+        .innerJoin(schema.lifecycleStages, and(eq(schema.lifecycleStages.pipelineId, schema.lifecyclePipelines.id), eq(schema.lifecycleStages.stageName, stageName)))
+        .where(eq(schema.lifecyclePipelines.taskId, taskId))
+        .limit(1)
+        .all();
+}
+/**
+ * Update pipeline's currentStageId.
+ *
+ * @param pipelineId - Pipeline ID to update
+ * @param currentStageId - New current stage identifier
+ * @param cwd - Working directory for database
+ */
+export async function updatePipelineCurrentStage(pipelineId, currentStageId, cwd) {
+    const db = await getDb(cwd);
+    await db
+        .update(schema.lifecyclePipelines)
+        .set({ currentStageId })
+        .where(eq(schema.lifecyclePipelines.id, pipelineId))
+        .run();
+}
+// =============================================================================
+// STAGE QUERIES
+// =============================================================================
+/**
+ * Get all stages for a pipeline, ordered by sequence.
+ *
+ * @param pipelineId - Pipeline ID
+ * @param cwd - Working directory for database
+ * @returns All stage rows for the pipeline
+ */
+export async function getStagesByPipelineId(pipelineId, cwd) {
+    const db = await getDb(cwd);
+    return db
+        .select()
+        .from(schema.lifecycleStages)
+        .where(eq(schema.lifecycleStages.pipelineId, pipelineId))
+        .orderBy(asc(schema.lifecycleStages.sequence))
+        .all();
+}
+/**
+ * Update a stage's status to 'in_progress' and clear block fields.
+ *
+ * @param stageId - Stage ID to update
+ * @param startedAt - ISO timestamp for when the stage started
+ * @param cwd - Working directory for database
+ */
+export async function activateStage(stageId, startedAt, cwd) {
+    const db = await getDb(cwd);
+    await db
+        .update(schema.lifecycleStages)
+        .set({
+        status: 'in_progress',
+        startedAt,
+        blockedAt: null,
+        blockReason: null,
+    })
+        .where(eq(schema.lifecycleStages.id, stageId))
+        .run();
+}
+/**
+ * Find pipeline with current stage (no task join) by taskId.
+ * Used by checkBlockedStageDetails.
+ *
+ * @param taskId - Task ID
+ * @param cwd - Working directory for database
+ * @returns Matching rows
+ */
+export async function findPipelineWithCurrentStage(taskId, cwd) {
+    const db = await getDb(cwd);
+    return db
+        .select({
+        pipeline: schema.lifecyclePipelines,
+        stageRecord: schema.lifecycleStages,
+    })
+        .from(schema.lifecyclePipelines)
+        .innerJoin(schema.lifecycleStages, eq(schema.lifecycleStages.pipelineId, schema.lifecyclePipelines.id))
+        .where(and(eq(schema.lifecyclePipelines.taskId, taskId), eq(schema.lifecycleStages.stageName, sql `${schema.lifecyclePipelines.currentStageId}`)))
+        .limit(1)
+        .all();
+}
+// =============================================================================
+// GATE RESULT QUERIES
+// =============================================================================
+/**
+ * Get gate results for a stage, ordered by checkedAt descending.
+ *
+ * @param stageId - Stage ID
+ * @param cwd - Working directory for database
+ * @returns Gate result rows
+ */
+export async function getGateResultsByStageId(stageId, cwd) {
+    const db = await getDb(cwd);
+    return db
+        .select()
+        .from(schema.lifecycleGateResults)
+        .where(eq(schema.lifecycleGateResults.stageId, stageId))
+        .orderBy(desc(schema.lifecycleGateResults.checkedAt))
+        .all();
+}
+/**
+ * Get gate results for a stage without ordering (for simple checks).
+ *
+ * @param stageId - Stage ID
+ * @param cwd - Working directory for database
+ * @returns Gate result rows
+ */
+export async function getGateResultsByStageIdUnordered(stageId, cwd) {
+    const db = await getDb(cwd);
+    return db
+        .select()
+        .from(schema.lifecycleGateResults)
+        .where(eq(schema.lifecycleGateResults.stageId, stageId))
+        .all();
+}
+// =============================================================================
+// EVIDENCE QUERIES
+// =============================================================================
+/**
+ * Get evidence for a stage, ordered by recordedAt descending.
+ *
+ * @param stageId - Stage ID
+ * @param cwd - Working directory for database
+ * @returns Evidence rows
+ */
+export async function getEvidenceByStageId(stageId, cwd) {
+    const db = await getDb(cwd);
+    return db
+        .select()
+        .from(schema.lifecycleEvidence)
+        .where(eq(schema.lifecycleEvidence.stageId, stageId))
+        .orderBy(desc(schema.lifecycleEvidence.recordedAt))
+        .all();
+}
+// =============================================================================
+// TRANSITION QUERIES & MUTATIONS
+// =============================================================================
+/**
+ * Get recent transitions for a pipeline, ordered by createdAt descending.
+ *
+ * @param pipelineId - Pipeline ID
+ * @param limit - Max rows to return (default: 10)
+ * @param cwd - Working directory for database
+ * @returns Transition rows
+ */
+export async function getRecentTransitions(pipelineId, limit = 10, cwd) {
+    const db = await getDb(cwd);
+    return db
+        .select()
+        .from(schema.lifecycleTransitions)
+        .where(eq(schema.lifecycleTransitions.pipelineId, pipelineId))
+        .orderBy(desc(schema.lifecycleTransitions.createdAt))
+        .limit(limit)
+        .all();
+}
+/**
+ * Insert a new transition record.
+ *
+ * @param transition - Transition data to insert
+ * @param cwd - Working directory for database
+ */
+export async function insertTransition(transition, cwd) {
+    const db = await getDb(cwd);
+    await db.insert(schema.lifecycleTransitions).values(transition).run();
+}
+//# sourceMappingURL=lifecycle-store.js.map

package/dist/store/lifecycle-store.js.map

@@ -0,0 +1 @@
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