@cleocode/core 2026.3.76 → 2026.4.0

package/dist/store/db-helpers.js

@@ -0,0 +1,224 @@
+/**
+ * Shared database helper functions for SQLite store modules.
+ *
+ * Consolidates upsert and dependency patterns used across
+ * sqlite-data-accessor.ts, task-store.ts, and session-store.ts.
+ *
+ * @epic T4454
+ */
+import { eq, inArray } from 'drizzle-orm';
+import * as schema from './tasks-schema.js';
+/**
+ * Upsert a single task row into the tasks table.
+ * Handles both active task upsert and archived task upsert via optional archiveFields.
+ *
+ * Defensively nulls out parentId if it references a non-existent task,
+ * preventing orphaned FK violations from blocking bulk operations (T5034).
+ */
+export async function upsertTask(db, row, archiveFields) {
+    // Defensive: null out parentId if it references a non-existent task (T5034)
+    if (row.parentId) {
+        const parent = await db
+            .select({ id: schema.tasks.id })
+            .from(schema.tasks)
+            .where(eq(schema.tasks.id, row.parentId))
+            .limit(1)
+            .all();
+        if (parent.length === 0) {
+            row = { ...row, parentId: null };
+        }
+    }
+    const values = archiveFields ? { ...row, ...archiveFields, status: 'archived' } : row;
+    const set = {
+        title: row.title,
+        description: row.description,
+        status: archiveFields ? 'archived' : row.status,
+        priority: row.priority,
+        type: row.type,
+        parentId: row.parentId,
+        phase: row.phase,
+        size: row.size,
+        position: row.position,
+        positionVersion: row.positionVersion,
+        labelsJson: row.labelsJson,
+        notesJson: row.notesJson,
+        acceptanceJson: row.acceptanceJson,
+        filesJson: row.filesJson,
+        origin: row.origin,
+        blockedBy: row.blockedBy,
+        epicLifecycle: row.epicLifecycle,
+        noAutoComplete: row.noAutoComplete,
+        createdAt: row.createdAt,
+        updatedAt: row.updatedAt,
+        completedAt: row.completedAt,
+        cancelledAt: row.cancelledAt,
+        cancellationReason: row.cancellationReason,
+        verificationJson: row.verificationJson,
+        createdBy: row.createdBy,
+        modifiedBy: row.modifiedBy,
+        sessionId: row.sessionId,
+        // T060: pipeline stage name (RCASD-IVTR+C)
+        pipelineStage: row.pipelineStage ?? null,
+        assignee: row.assignee ?? null,
+        // Always include archive metadata so unarchive clears stale values (T5034)
+        archivedAt: archiveFields?.archivedAt ?? null,
+        archiveReason: archiveFields?.archiveReason ?? null,
+        cycleTimeDays: archiveFields?.cycleTimeDays ?? null,
+    };
+    await db
+        .insert(schema.tasks)
+        .values(values)
+        .onConflictDoUpdate({ target: schema.tasks.id, set })
+        .run();
+}
+/**
+ * Upsert a single session row into the sessions table.
+ */
+export async function upsertSession(db, session) {
+    const sessionName = session.name || `session-${session.id}`;
+    const values = {
+        id: session.id,
+        name: sessionName,
+        status: session.status,
+        scopeJson: JSON.stringify(session.scope ?? { type: 'global' }),
+        currentTask: session.taskWork?.taskId ?? null,
+        taskStartedAt: session.taskWork?.setAt ?? null,
+        agent: session.agent ?? null,
+        notesJson: session.notes ? JSON.stringify(session.notes) : '[]',
+        tasksCompletedJson: session.tasksCompleted ? JSON.stringify(session.tasksCompleted) : '[]',
+        tasksCreatedJson: session.tasksCreated ? JSON.stringify(session.tasksCreated) : '[]',
+        handoffJson: session.handoffJson ?? null,
+        startedAt: session.startedAt,
+        endedAt: session.endedAt ?? null,
+        // Session chain fields (T4959)
+        previousSessionId: session.previousSessionId ?? null,
+        nextSessionId: session.nextSessionId ?? null,
+        agentIdentifier: session.agentIdentifier ?? null,
+        handoffConsumedAt: session.handoffConsumedAt ?? null,
+        handoffConsumedBy: session.handoffConsumedBy ?? null,
+        debriefJson: session.debriefJson ?? null,
+        // Session stats fields
+        statsJson: session.stats ? JSON.stringify(session.stats) : null,
+        resumeCount: session.resumeCount ?? null,
+        gradeMode: session.gradeMode ? 1 : null,
+    };
+    const { id: _id, ...setFields } = values;
+    await db
+        .insert(schema.sessions)
+        .values(values)
+        .onConflictDoUpdate({ target: schema.sessions.id, set: setFields })
+        .run();
+}
+/**
+ * Update dependencies for a task: delete existing, then re-insert.
+ * Optionally filters by a set of valid IDs.
+ */
+export async function updateDependencies(db, taskId, depends, validIds) {
+    await db.delete(schema.taskDependencies).where(eq(schema.taskDependencies.taskId, taskId)).run();
+    for (const depId of depends) {
+        if (!validIds || validIds.has(depId)) {
+            await db
+                .insert(schema.taskDependencies)
+                .values({ taskId, dependsOn: depId })
+                .onConflictDoNothing()
+                .run();
+        }
+    }
+}
+/**
+ * Batch-update dependencies for multiple tasks in two bulk SQL operations.
+ * Replaces per-task updateDependencies() loops with:
+ * 1. Single DELETE for all task IDs
+ * 2. Single INSERT for all dependency rows
+ *
+ * Callers are responsible for wrapping this in a transaction if needed.
+ */
+export async function batchUpdateDependencies(db, tasks, validIds) {
+    if (tasks.length === 0)
+        return;
+    const allTaskIds = tasks.map((t) => t.taskId);
+    // Single DELETE: remove all existing dependencies for these tasks
+    await db
+        .delete(schema.taskDependencies)
+        .where(inArray(schema.taskDependencies.taskId, allTaskIds))
+        .run();
+    // Collect all valid dependency rows
+    const allDepRows = [];
+    for (const { taskId, deps } of tasks) {
+        for (const depId of deps) {
+            if (!validIds || validIds.has(depId)) {
+                allDepRows.push({ taskId, dependsOn: depId });
+            }
+        }
+    }
+    // Single INSERT for all dependency rows
+    if (allDepRows.length > 0) {
+        await db.insert(schema.taskDependencies).values(allDepRows).onConflictDoNothing().run();
+    }
+}
+/**
+ * Batch-load dependencies for a list of tasks and apply them in-place.
+ * Uses inArray for efficient querying. Optionally filters by a set of valid IDs.
+ */
+export async function loadDependenciesForTasks(db, tasks, validationIds) {
+    if (tasks.length === 0)
+        return;
+    const taskIds = tasks.map((t) => t.id);
+    const taskIdSet = validationIds ?? new Set(taskIds);
+    const allDeps = await db
+        .select()
+        .from(schema.taskDependencies)
+        .where(inArray(schema.taskDependencies.taskId, taskIds))
+        .all();
+    const depMap = new Map();
+    for (const dep of allDeps) {
+        if (taskIdSet.has(dep.dependsOn)) {
+            let arr = depMap.get(dep.taskId);
+            if (!arr) {
+                arr = [];
+                depMap.set(dep.taskId, arr);
+            }
+            arr.push(dep.dependsOn);
+        }
+    }
+    for (const task of tasks) {
+        const deps = depMap.get(task.id);
+        if (deps && deps.length > 0) {
+            task.depends = deps;
+        }
+    }
+}
+/**
+ * Batch-load relations for a list of tasks and apply them in-place.
+ * Mirrors loadDependenciesForTasks pattern for task_relations table (T5168).
+ */
+export async function loadRelationsForTasks(db, tasks) {
+    if (tasks.length === 0)
+        return;
+    const taskIds = tasks.map((t) => t.id);
+    const allRels = await db
+        .select()
+        .from(schema.taskRelations)
+        .where(inArray(schema.taskRelations.taskId, taskIds))
+        .all();
+    const relMap = new Map();
+    for (const rel of allRels) {
+        let arr = relMap.get(rel.taskId);
+        if (!arr) {
+            arr = [];
+            relMap.set(rel.taskId, arr);
+        }
+        arr.push({
+            taskId: rel.relatedTo,
+            type: rel.relationType,
+            reason: rel.reason ?? undefined,
+        });
+    }
+    for (const task of tasks) {
+        const relations = relMap.get(task.id);
+        if (relations && relations.length > 0) {
+            task.relates = relations;
+        }
+    }
+}
+//# sourceMappingURL=db-helpers.js.map

package/dist/store/db-helpers.js.map

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package/dist/store/export.js

@@ -0,0 +1,155 @@
+/**
+ * Export package generation for task data interchange.
+ * Ported from lib/data/export.sh
+ *
+ * @epic T4454
+ * @task T4530
+ */
+import { createHash } from 'node:crypto';
+/** Export format version. */
+const EXPORT_FORMAT_VERSION = '1.0.0';
+/**
+ * Calculate SHA-256 checksum for export integrity (truncated to 16 hex chars).
+ */
+export function calculateExportChecksum(tasksJson) {
+    const canonical = JSON.stringify(JSON.parse(tasksJson));
+    return createHash('sha256').update(canonical).digest('hex').slice(0, 16);
+}
+/**
+ * Verify export package checksum.
+ */
+export function verifyExportChecksum(pkg) {
+    const tasksJson = JSON.stringify(pkg.tasks);
+    const calculated = calculateExportChecksum(tasksJson);
+    return pkg._meta.checksum === calculated;
+}
+/**
+ * Build ID map from tasks.
+ */
+export function buildIdMap(tasks) {
+    const map = {};
+    for (const task of tasks) {
+        map[task.id] = {
+            type: task.type ?? 'task',
+            title: task.title,
+            status: task.status,
+            parentId: task.parentId ?? null,
+            depends: task.depends ?? [],
+        };
+    }
+    return map;
+}
+/**
+ * Build relationship graph from tasks.
+ */
+export function buildRelationshipGraph(tasks) {
+    const exportedIds = new Set(tasks.map((t) => t.id));
+    const hierarchy = {};
+    const dependencies = {};
+    for (const task of tasks) {
+        // Hierarchy
+        if (task.parentId && exportedIds.has(task.parentId)) {
+            if (!hierarchy[task.parentId])
+                hierarchy[task.parentId] = [];
+            hierarchy[task.parentId].push(task.id);
+        }
+        // Dependencies
+        if (task.depends?.length) {
+            const internalDeps = task.depends.filter((d) => exportedIds.has(d));
+            if (internalDeps.length > 0) {
+                dependencies[task.id] = internalDeps;
+            }
+        }
+    }
+    // Roots: tasks with no parent in export and no deps in export
+    const roots = tasks
+        .filter((t) => {
+        const hasParentInExport = t.parentId && exportedIds.has(t.parentId);
+        const hasDepsInExport = t.depends?.some((d) => exportedIds.has(d));
+        return !hasParentInExport && !hasDepsInExport;
+    })
+        .map((t) => t.id);
+    return { hierarchy, dependencies, roots };
+}
+/**
+ * Build a complete export package.
+ */
+export function buildExportPackage(tasks, options) {
+    const now = new Date().toISOString();
+    const projectName = options.projectName ?? 'unknown';
+    const maxId = tasks.reduce((max, t) => {
+        const num = parseInt(t.id.replace('T', ''), 10);
+        return num > max ? num : max;
+    }, 0);
+    const idMap = buildIdMap(tasks);
+    const relationshipGraph = buildRelationshipGraph(tasks);
+    const tasksJson = JSON.stringify(tasks);
+    const checksum = calculateExportChecksum(tasksJson);
+    return {
+        $schema: 'https://cleo-dev.com/schemas/v1/export-package.schema.json',
+        _meta: {
+            format: 'cleo-export',
+            version: EXPORT_FORMAT_VERSION,
+            exportedAt: now,
+            source: {
+                project: projectName,
+                cleo_version: options.cleoVersion ?? '0.95.0',
+                nextId: maxId + 1,
+            },
+            checksum,
+            taskCount: tasks.length,
+            exportMode: options.mode,
+        },
+        selection: {
+            mode: options.mode,
+            rootTaskIds: options.rootTaskIds,
+            includeChildren: options.includeChildren,
+            filters: options.filters,
+        },
+        idMap,
+        tasks,
+        relationshipGraph,
+    };
+}
+/**
+ * Export a single task.
+ */
+export function exportSingle(taskId, allTasks, projectName) {
+    const task = allTasks.find((t) => t.id === taskId);
+    if (!task)
+        return null;
+    return buildExportPackage([task], {
+        mode: 'single',
+        rootTaskIds: [taskId],
+        includeChildren: false,
+        projectName,
+    });
+}
+/**
+ * Export a subtree (task + all descendants).
+ */
+export function exportSubtree(rootId, allTasks, projectName) {
+    const root = allTasks.find((t) => t.id === rootId);
+    if (!root)
+        return null;
+    // Collect all descendants via BFS
+    const collected = new Map();
+    const queue = [rootId];
+    while (queue.length > 0) {
+        const id = queue.shift();
+        const task = allTasks.find((t) => t.id === id);
+        if (!task || collected.has(id))
+            continue;
+        collected.set(id, task);
+        const children = allTasks.filter((t) => t.parentId === id);
+        queue.push(...children.map((c) => c.id));
+    }
+    const tasks = [...collected.values()];
+    return buildExportPackage(tasks, {
+        mode: 'subtree',
+        rootTaskIds: [rootId],
+        includeChildren: true,
+        projectName,
+    });
+}
+//# sourceMappingURL=export.js.map

package/dist/store/export.js.map

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package/dist/store/file-utils.js

@@ -0,0 +1,270 @@
+/**
+ * File utility helpers for CLEO data access.
+ *
+ * File utility helpers for CLEO data access including atomic writes,
+ * file locking, and backup rotation.
+ *
+ * @task T4833
+ * @epic T4654
+ */
+import { randomBytes } from 'node:crypto';
+import { existsSync, mkdirSync, readdirSync, readFileSync, renameSync, unlinkSync, writeFileSync, } from 'node:fs';
+import { basename, dirname, join } from 'node:path';
+import * as lockfile from 'proper-lockfile';
+/**
+ * Maximum number of operational backups to keep.
+ */
+const MAX_BACKUPS = 10;
+/**
+ * Create a numbered backup of a file (Tier 1 operational backup).
+ */
+function rotateBackup(filePath) {
+    const dir = dirname(filePath);
+    const name = basename(filePath);
+    const backupDir = join(dir, '.backups');
+    if (!existsSync(backupDir)) {
+        mkdirSync(backupDir, { recursive: true });
+    }
+    for (let i = MAX_BACKUPS; i >= 1; i--) {
+        const current = join(backupDir, `${name}.${i}`);
+        if (i === MAX_BACKUPS) {
+            try {
+                unlinkSync(current);
+            }
+            catch {
+                /* May not exist */
+            }
+        }
+        else {
+            const next = join(backupDir, `${name}.${i + 1}`);
+            try {
+                if (existsSync(current))
+                    renameSync(current, next);
+            }
+            catch {
+                /* Ignore rename errors */
+            }
+        }
+    }
+    try {
+        const content = readFileSync(filePath, 'utf-8');
+        writeFileSync(join(backupDir, `${name}.1`), content, 'utf-8');
+    }
+    catch {
+        /* Non-fatal */
+    }
+}
+/**
+ * Write a JSON file atomically with backup rotation.
+ *
+ * Pattern: write temp -> backup original -> rename temp to target
+ *
+ * @param filePath - Target file path
+ * @param data - Data to serialize as JSON
+ * @param indent - JSON indentation (default: 2 spaces)
+ */
+export function writeJsonFileAtomic(filePath, data, indent = 2) {
+    const dir = dirname(filePath);
+    const tempPath = join(dir, `.${basename(filePath)}.${randomBytes(6).toString('hex')}.tmp`);
+    const content = JSON.stringify(data, null, indent) + '\n';
+    writeFileSync(tempPath, content, 'utf-8');
+    try {
+        if (existsSync(filePath)) {
+            rotateBackup(filePath);
+        }
+        renameSync(tempPath, filePath);
+    }
+    catch (error) {
+        try {
+            unlinkSync(tempPath);
+        }
+        catch {
+            /* Ignore cleanup errors */
+        }
+        throw error;
+    }
+}
+/**
+ * Read a JSON file, returning parsed content or null if not found.
+ *
+ * @param filePath - Path to the JSON file
+ */
+export function readJsonFile(filePath) {
+    try {
+        const content = readFileSync(filePath, 'utf-8');
+        return JSON.parse(content);
+    }
+    catch (error) {
+        if (error.code === 'ENOENT') {
+            return null;
+        }
+        throw error;
+    }
+}
+/**
+ * Get the path to a CLEO data file within a project root.
+ *
+ * @param projectRoot - Root directory of the project
+ * @param filename - Filename within .cleo/ directory
+ */
+export function getDataPath(projectRoot, filename) {
+    return join(projectRoot, '.cleo', filename);
+}
+/**
+ * Resolve the project root directory.
+ * Checks CLEO_ROOT env, then falls back to cwd.
+ */
+export function resolveProjectRoot() {
+    return process.env['CLEO_ROOT'] || process.cwd();
+}
+/**
+ * Default lock options matching bash flock behavior
+ */
+const LOCK_OPTIONS = {
+    retries: {
+        retries: 5,
+        factor: 2,
+        minTimeout: 100,
+        maxTimeout: 5000,
+    },
+    stale: 30000, // 30s stale lock timeout
+};
+/**
+ * Lock ordering to prevent deadlocks.
+ * Always acquire locks in this order.
+ */
+const LOCK_ORDER = {
+    'tasks.db': 1,
+    'config.json': 2,
+};
+function getLockPriority(filePath) {
+    const name = basename(filePath);
+    return LOCK_ORDER[name] ?? 99;
+}
+/**
+ * Read and write a JSON file with exclusive locking.
+ *
+ * Acquires a cross-process lock, reads current state, applies the
+ * transform function, validates, and writes back atomically.
+ *
+ * @param filePath - File to lock and modify
+ * @param transform - Function that receives current data and returns new data
+ * @returns The transformed data
+ */
+export async function withLock(filePath, transform) {
+    const dir = dirname(filePath);
+    if (!existsSync(dir)) {
+        mkdirSync(dir, { recursive: true });
+    }
+    // Ensure file exists for locking (proper-lockfile needs the file to exist)
+    if (!existsSync(filePath)) {
+        writeFileSync(filePath, '', 'utf-8');
+    }
+    let release;
+    try {
+        release = await lockfile.lock(filePath, LOCK_OPTIONS);
+        const current = readJsonFile(filePath);
+        const updated = transform(current);
+        writeJsonFileAtomic(filePath, updated);
+        return updated;
+    }
+    finally {
+        if (release) {
+            await release();
+        }
+    }
+}
+/**
+ * Acquire a file lock and execute an operation.
+ * Unlike withLock, this doesn't read/write the file - caller manages I/O.
+ * The return type R is independent of the file content type.
+ */
+export async function withFileLock(filePath, operation) {
+    const dir = dirname(filePath);
+    if (!existsSync(dir)) {
+        mkdirSync(dir, { recursive: true });
+    }
+    if (!existsSync(filePath)) {
+        writeFileSync(filePath, '', 'utf-8');
+    }
+    let release;
+    try {
+        release = await lockfile.lock(filePath, LOCK_OPTIONS);
+        return await operation();
+    }
+    finally {
+        if (release) {
+            await release();
+        }
+    }
+}
+/**
+ * Acquire locks on multiple files in correct order.
+ * Used for operations that need to modify multiple files atomically
+ * (e.g., coordinated updates across task data and config).
+ *
+ * @param filePaths - Files to lock
+ * @param operation - Function to execute while locks are held
+ */
+export async function withMultiLock(filePaths, operation) {
+    // Sort by lock priority to prevent deadlocks
+    const sorted = [...filePaths].sort((a, b) => getLockPriority(a) - getLockPriority(b));
+    const releases = [];
+    try {
+        // Acquire locks in order
+        for (const fp of sorted) {
+            if (!existsSync(dirname(fp))) {
+                mkdirSync(dirname(fp), { recursive: true });
+            }
+            if (!existsSync(fp)) {
+                writeFileSync(fp, '', 'utf-8');
+            }
+            const release = await lockfile.lock(fp, LOCK_OPTIONS);
+            releases.push(release);
+        }
+        return await operation();
+    }
+    finally {
+        // Release in reverse order
+        for (const release of releases.reverse()) {
+            try {
+                await release();
+            }
+            catch {
+                // Ignore release errors
+            }
+        }
+    }
+}
+/**
+ * Check if a CLEO project directory exists at the given path
+ */
+export function isProjectInitialized(projectRoot) {
+    const cleoDir = join(projectRoot, '.cleo');
+    return existsSync(cleoDir) && existsSync(join(cleoDir, 'tasks.db'));
+}
+/**
+ * List backup files for a given data file
+ */
+export function listBackups(filePath) {
+    const dir = dirname(filePath);
+    const name = basename(filePath);
+    const backupDir = join(dir, '.backups');
+    if (!existsSync(backupDir)) {
+        return [];
+    }
+    try {
+        return readdirSync(backupDir)
+            .filter((f) => f.startsWith(`${name}.`) && /\.\d+$/.test(f))
+            .sort((a, b) => {
+            const numA = parseInt(a.split('.').pop(), 10);
+            const numB = parseInt(b.split('.').pop(), 10);
+            return numA - numB;
+        })
+            .map((f) => join(backupDir, f));
+    }
+    catch {
+        return [];
+    }
+}
+//# sourceMappingURL=file-utils.js.map

package/dist/store/file-utils.js.map

@@ -0,0 +1 @@
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