backup: Phase 1 agent work (security, persistence, batch endpoint)
This is a backup of all work done by the 3 Phase 1 agents: Agent A - Command Injection Fix (Issue #354): - Fixed command injection in BranchManager.ts - Fixed unnecessary shell usage in bun-path.ts - Added comprehensive security test suite - Created SECURITY.md and SECURITY_AUDIT_REPORT.md Agent B - Observation Persistence Fix (Issue #353): - Added PendingMessageStore from PR #335 - Integrated persistent queue into SessionManager - Modified SDKAgent to mark messages complete - Updated SessionStore with pending_messages migration - Updated worker-types.ts with new interfaces Agent C - Batch Endpoint Verification (Issue #348): - Created batch-observations.test.ts - Updated worker-service.mdx documentation Also includes: - Documentation context files (biomimetic, windows struggles) - Build artifacts from agent testing This work will be re-evaluated after v7.3.0 release.
This commit is contained in:
Alex Newman
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import { Database } from './sqlite-compat.js';
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import type { PendingMessage } from '../worker-types.js';
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/**
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* Persistent pending message record from database
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*/
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export interface PersistentPendingMessage {
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id: number;
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session_db_id: number;
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claude_session_id: string;
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message_type: 'observation' | 'summarize';
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tool_name: string | null;
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tool_input: string | null;
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tool_response: string | null;
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cwd: string | null;
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last_user_message: string | null;
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last_assistant_message: string | null;
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prompt_number: number | null;
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status: 'pending' | 'processing' | 'processed' | 'failed';
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retry_count: number;
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created_at_epoch: number;
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started_processing_at_epoch: number | null;
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completed_at_epoch: number | null;
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}
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/**
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* PendingMessageStore - Persistent work queue for SDK messages
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*
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* Messages are persisted before processing and marked complete after success.
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* This enables recovery from SDK hangs and worker crashes.
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*
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* Lifecycle:
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* 1. enqueue() - Message persisted with status 'pending'
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* 2. markProcessing() - Status changes to 'processing' when yielded to SDK
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* 3. markProcessed() - Status changes to 'processed' after successful SDK response
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* 4. markFailed() - Status changes to 'failed' if max retries exceeded
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*
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* Recovery:
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* - resetStuckMessages() - Moves 'processing' messages back to 'pending' if stuck
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* - getSessionsWithPendingMessages() - Find sessions that need recovery on startup
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*/
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export class PendingMessageStore {
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private db: Database;
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private maxRetries: number;
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constructor(db: Database, maxRetries: number = 3) {
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this.db = db;
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this.maxRetries = maxRetries;
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}
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/**
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* Enqueue a new message (persist before processing)
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* @returns The database ID of the persisted message
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*/
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enqueue(sessionDbId: number, claudeSessionId: string, message: PendingMessage): number {
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const now = Date.now();
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const stmt = this.db.prepare(`
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INSERT INTO pending_messages (
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session_db_id, claude_session_id, message_type,
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tool_name, tool_input, tool_response, cwd,
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last_user_message, last_assistant_message,
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prompt_number, status, retry_count, created_at_epoch
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) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, 'pending', 0, ?)
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`);
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const result = stmt.run(
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sessionDbId,
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claudeSessionId,
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message.type,
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message.tool_name || null,
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message.tool_input ? JSON.stringify(message.tool_input) : null,
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message.tool_response ? JSON.stringify(message.tool_response) : null,
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message.cwd || null,
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message.last_user_message || null,
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message.last_assistant_message || null,
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message.prompt_number || null,
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now
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);
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return result.lastInsertRowid as number;
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}
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/**
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* Peek at oldest pending message for session (does NOT change status)
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* @returns The oldest pending message or null if none
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*/
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peekPending(sessionDbId: number): PersistentPendingMessage | null {
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const stmt = this.db.prepare(`
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SELECT * FROM pending_messages
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WHERE session_db_id = ? AND status = 'pending'
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ORDER BY id ASC
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LIMIT 1
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`);
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return stmt.get(sessionDbId) as PersistentPendingMessage | null;
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}
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/**
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* Get all pending messages for session (ordered by creation time)
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*/
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getAllPending(sessionDbId: number): PersistentPendingMessage[] {
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const stmt = this.db.prepare(`
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SELECT * FROM pending_messages
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WHERE session_db_id = ? AND status = 'pending'
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ORDER BY id ASC
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`);
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return stmt.all(sessionDbId) as PersistentPendingMessage[];
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}
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/**
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* Get all queue messages (for UI display)
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* Returns pending, processing, and failed messages (not processed - they're deleted)
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* Joins with sdk_sessions to get project name
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*/
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getQueueMessages(): (PersistentPendingMessage & { project: string | null })[] {
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const stmt = this.db.prepare(`
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SELECT pm.*, ss.project
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FROM pending_messages pm
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LEFT JOIN sdk_sessions ss ON pm.claude_session_id = ss.claude_session_id
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WHERE pm.status IN ('pending', 'processing', 'failed')
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ORDER BY
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CASE pm.status
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WHEN 'failed' THEN 0
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WHEN 'processing' THEN 1
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WHEN 'pending' THEN 2
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END,
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pm.created_at_epoch ASC
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`);
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return stmt.all() as (PersistentPendingMessage & { project: string | null })[];
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}
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/**
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* Get count of stuck messages (processing longer than threshold)
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*/
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getStuckCount(thresholdMs: number): number {
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const cutoff = Date.now() - thresholdMs;
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const stmt = this.db.prepare(`
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SELECT COUNT(*) as count FROM pending_messages
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WHERE status = 'processing' AND started_processing_at_epoch < ?
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`);
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const result = stmt.get(cutoff) as { count: number };
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return result.count;
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}
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/**
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* Retry a specific message (reset to pending)
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* Works for pending (re-queue), processing (reset stuck), and failed messages
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*/
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retryMessage(messageId: number): boolean {
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const stmt = this.db.prepare(`
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UPDATE pending_messages
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SET status = 'pending', started_processing_at_epoch = NULL
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WHERE id = ? AND status IN ('pending', 'processing', 'failed')
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`);
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const result = stmt.run(messageId);
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return result.changes > 0;
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}
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/**
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* Reset all processing messages for a session to pending
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* Used when force-restarting a stuck session
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*/
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resetProcessingToPending(sessionDbId: number): number {
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const stmt = this.db.prepare(`
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UPDATE pending_messages
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SET status = 'pending', started_processing_at_epoch = NULL
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WHERE session_db_id = ? AND status = 'processing'
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`);
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const result = stmt.run(sessionDbId);
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return result.changes;
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}
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/**
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* Abort a specific message (delete from queue)
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*/
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abortMessage(messageId: number): boolean {
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const stmt = this.db.prepare('DELETE FROM pending_messages WHERE id = ?');
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const result = stmt.run(messageId);
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return result.changes > 0;
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}
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/**
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* Retry all stuck messages at once
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*/
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retryAllStuck(thresholdMs: number): number {
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const cutoff = Date.now() - thresholdMs;
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const stmt = this.db.prepare(`
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UPDATE pending_messages
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SET status = 'pending', started_processing_at_epoch = NULL
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WHERE status = 'processing' AND started_processing_at_epoch < ?
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`);
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const result = stmt.run(cutoff);
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return result.changes;
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}
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/**
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* Get recently processed messages (for UI feedback)
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* Shows messages completed in the last N minutes so users can see their stuck items were processed
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*/
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getRecentlyProcessed(limit: number = 10, withinMinutes: number = 30): (PersistentPendingMessage & { project: string | null })[] {
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const cutoff = Date.now() - (withinMinutes * 60 * 1000);
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const stmt = this.db.prepare(`
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SELECT pm.*, ss.project
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FROM pending_messages pm
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LEFT JOIN sdk_sessions ss ON pm.claude_session_id = ss.claude_session_id
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WHERE pm.status = 'processed' AND pm.completed_at_epoch > ?
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ORDER BY pm.completed_at_epoch DESC
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LIMIT ?
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`);
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return stmt.all(cutoff, limit) as (PersistentPendingMessage & { project: string | null })[];
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}
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/**
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* Mark message as being processed (status: pending -> processing)
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*/
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markProcessing(messageId: number): void {
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const now = Date.now();
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const stmt = this.db.prepare(`
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UPDATE pending_messages
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SET status = 'processing', started_processing_at_epoch = ?
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WHERE id = ? AND status = 'pending'
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`);
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stmt.run(now, messageId);
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}
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/**
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* Mark message as successfully processed (status: processing -> processed)
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*/
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markProcessed(messageId: number): void {
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const now = Date.now();
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const stmt = this.db.prepare(`
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UPDATE pending_messages
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SET status = 'processed', completed_at_epoch = ?
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WHERE id = ? AND status = 'processing'
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`);
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stmt.run(now, messageId);
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}
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/**
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* Mark message as failed (status: processing -> failed or back to pending for retry)
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* If retry_count < maxRetries, moves back to 'pending' for retry
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* Otherwise marks as 'failed' permanently
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*/
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markFailed(messageId: number): void {
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const now = Date.now();
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// Get current retry count
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const msg = this.db.prepare('SELECT retry_count FROM pending_messages WHERE id = ?').get(messageId) as { retry_count: number } | undefined;
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if (!msg) return;
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if (msg.retry_count < this.maxRetries) {
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// Move back to pending for retry
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const stmt = this.db.prepare(`
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UPDATE pending_messages
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SET status = 'pending', retry_count = retry_count + 1, started_processing_at_epoch = NULL
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WHERE id = ?
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`);
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stmt.run(messageId);
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} else {
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// Max retries exceeded, mark as permanently failed
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const stmt = this.db.prepare(`
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UPDATE pending_messages
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SET status = 'failed', completed_at_epoch = ?
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WHERE id = ?
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`);
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stmt.run(now, messageId);
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}
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}
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/**
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* Reset stuck messages (processing -> pending if stuck longer than threshold)
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* @param thresholdMs Messages processing longer than this are considered stuck (0 = reset all)
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* @returns Number of messages reset
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*/
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resetStuckMessages(thresholdMs: number): number {
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const cutoff = thresholdMs === 0 ? Date.now() : Date.now() - thresholdMs;
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const stmt = this.db.prepare(`
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UPDATE pending_messages
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SET status = 'pending', started_processing_at_epoch = NULL
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WHERE status = 'processing' AND started_processing_at_epoch < ?
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`);
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const result = stmt.run(cutoff);
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return result.changes;
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}
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/**
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* Get count of pending messages for a session
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*/
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getPendingCount(sessionDbId: number): number {
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const stmt = this.db.prepare(`
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SELECT COUNT(*) as count FROM pending_messages
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WHERE session_db_id = ? AND status IN ('pending', 'processing')
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`);
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const result = stmt.get(sessionDbId) as { count: number };
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return result.count;
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}
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/**
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* Check if any session has pending work
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*/
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hasAnyPendingWork(): boolean {
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const stmt = this.db.prepare(`
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SELECT COUNT(*) as count FROM pending_messages
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WHERE status IN ('pending', 'processing')
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`);
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const result = stmt.get() as { count: number };
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return result.count > 0;
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}
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/**
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* Get all session IDs that have pending messages (for recovery on startup)
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*/
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getSessionsWithPendingMessages(): number[] {
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const stmt = this.db.prepare(`
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SELECT DISTINCT session_db_id FROM pending_messages
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WHERE status IN ('pending', 'processing')
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`);
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const results = stmt.all() as { session_db_id: number }[];
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return results.map(r => r.session_db_id);
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}
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/**
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* Get session info for a pending message (for recovery)
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*/
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getSessionInfoForMessage(messageId: number): { sessionDbId: number; claudeSessionId: string } | null {
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const stmt = this.db.prepare(`
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SELECT session_db_id, claude_session_id FROM pending_messages WHERE id = ?
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`);
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const result = stmt.get(messageId) as { session_db_id: number; claude_session_id: string } | undefined;
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return result ? { sessionDbId: result.session_db_id, claudeSessionId: result.claude_session_id } : null;
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}
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/**
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* Cleanup old processed messages (retention policy)
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* @param retentionMs Delete processed messages older than this (0 = delete all processed)
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* @returns Number of messages deleted
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*/
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cleanupProcessed(retentionMs: number): number {
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const cutoff = retentionMs === 0 ? Date.now() : Date.now() - retentionMs;
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const stmt = this.db.prepare(`
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DELETE FROM pending_messages
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WHERE status = 'processed' AND completed_at_epoch < ?
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`);
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const result = stmt.run(cutoff);
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return result.changes;
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}
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/**
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* Convert a PersistentPendingMessage back to PendingMessage format
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*/
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toPendingMessage(persistent: PersistentPendingMessage): PendingMessage {
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return {
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type: persistent.message_type,
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tool_name: persistent.tool_name || undefined,
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tool_input: persistent.tool_input ? JSON.parse(persistent.tool_input) : undefined,
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tool_response: persistent.tool_response ? JSON.parse(persistent.tool_response) : undefined,
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prompt_number: persistent.prompt_number || undefined,
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cwd: persistent.cwd || undefined,
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last_user_message: persistent.last_user_message || undefined,
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last_assistant_message: persistent.last_assistant_message || undefined
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};
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}
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}
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