@vladimir-ks/aigile 0.2.6 → 0.2.7

package/dist/bin/aigile.js

@@ -426,7 +426,8 @@ __export(connection_exports, {
   run: () => run,
   runMigrations: () => runMigrations,
   saveDatabase: () => saveDatabase,
-  tagFileReviewed: () => tagFileReviewed
+  tagFileReviewed: () => tagFileReviewed,
+  transaction: () => transaction
 });
 import initSqlJs from "sql.js";
 import { existsSync as existsSync2, readFileSync as readFileSync2, writeFileSync as writeFileSync2, mkdirSync as mkdirSync2 } from "fs";
@@ -460,16 +461,33 @@ function getDatabase() {
   }
   return db;
 }
-function saveDatabase() {
-  if (db && dbPath) {
+function saveDatabase(retries = 3) {
+  if (!db || !dbPath) {
+    return;
+  }
+  let lastError = null;
+  for (let attempt = 0; attempt < retries; attempt++) {
     try {
       const data2 = db.export();
       const buffer = Buffer.from(data2);
       writeFileSync2(dbPath, buffer);
+      return;
     } catch (err) {
-      console.error(`[${(/* @__PURE__ */ new Date()).toISOString()}] Database save error: ${err}`);
+      lastError = err instanceof Error ? err : new Error(String(err));
+      console.error(
+        `[${(/* @__PURE__ */ new Date()).toISOString()}] Database save attempt ${attempt + 1}/${retries} failed: ${lastError.message}`
+      );
+      if (attempt < retries - 1) {
+        const delay = Math.min(100 * Math.pow(2, attempt), 1e3);
+        const start = Date.now();
+        while (Date.now() - start < delay) {
+        }
+      }
     }
   }
+  throw new Error(
+    `Failed to save database after ${retries} attempts: ${lastError?.message || "Unknown error"}`
+  );
 }
 function closeDatabase() {
   if (db) {
@@ -497,7 +515,36 @@ function queryOne(sql, params = []) {
 function run(sql, params = []) {
   const database = getDatabase();
   database.run(sql, params);
-  saveDatabase();
+  if (transactionDepth === 0) {
+    saveDatabase();
+  }
+}
+async function transaction(callback) {
+  const database = getDatabase();
+  const isOutermost = transactionDepth === 0;
+  transactionDepth++;
+  try {
+    if (isOutermost) {
+      database.run("BEGIN TRANSACTION");
+    }
+    const result = await callback();
+    if (isOutermost) {
+      database.run("COMMIT");
+      saveDatabase();
+    }
+    return result;
+  } catch (err) {
+    if (isOutermost) {
+      try {
+        database.run("ROLLBACK");
+      } catch (rollbackErr) {
+        console.error(`[${(/* @__PURE__ */ new Date()).toISOString()}] Rollback failed: ${rollbackErr}`);
+      }
+    }
+    throw err;
+  } finally {
+    transactionDepth--;
+  }
 }
 function initializeSchema(database) {
   database.run(`
@@ -829,7 +876,9 @@ function initializeSchema(database) {
     )
   `);
   database.run(`CREATE INDEX IF NOT EXISTS idx_session_files_session ON session_files(session_id)`);
-  database.run(`CREATE INDEX IF NOT EXISTS idx_session_files_document ON session_files(document_id)`);
+  database.run(
+    `CREATE INDEX IF NOT EXISTS idx_session_files_document ON session_files(document_id)`
+  );
   database.run(`CREATE INDEX IF NOT EXISTS idx_session_files_chunk ON session_files(chunk_id)`);
   database.run(`CREATE INDEX IF NOT EXISTS idx_session_files_report ON session_files(report_path)`);
   database.run(`CREATE INDEX IF NOT EXISTS idx_chunks_session ON chunks(session_id)`);
@@ -849,10 +898,11 @@ function getNextKey(projectKey) {
       [nextValue, projectKey]
     );
   } else {
-    run(
-      `INSERT INTO key_sequences (id, prefix, current_value) VALUES (?, ?, ?)`,
-      [generateId(), projectKey, nextValue]
-    );
+    run(`INSERT INTO key_sequences (id, prefix, current_value) VALUES (?, ?, ?)`, [
+      generateId(),
+      projectKey,
+      nextValue
+    ]);
   }
   return `${projectKey}-${nextValue}`;
 }
@@ -874,10 +924,9 @@ function getChunk(chunkId) {
   return queryOne("SELECT * FROM chunks WHERE id = ?", [chunkId]);
 }
 function getSessionChunks(sessionId) {
-  return queryAll(
-    "SELECT * FROM chunks WHERE session_id = ? ORDER BY created_at",
-    [sessionId]
-  );
+  return queryAll("SELECT * FROM chunks WHERE session_id = ? ORDER BY created_at", [
+    sessionId
+  ]);
 }
 function assignFilesToChunk(chunkId, files) {
   const chunk = getChunk(chunkId);
@@ -886,10 +935,10 @@ function assignFilesToChunk(chunkId, files) {
   }
   const existing = chunk.assigned_files ? JSON.parse(chunk.assigned_files) : [];
   const merged = [.../* @__PURE__ */ new Set([...existing, ...files])];
-  run(
-    `UPDATE chunks SET assigned_files = ?, updated_at = datetime('now') WHERE id = ?`,
-    [JSON.stringify(merged), chunkId]
-  );
+  run(`UPDATE chunks SET assigned_files = ?, updated_at = datetime('now') WHERE id = ?`, [
+    JSON.stringify(merged),
+    chunkId
+  ]);
 }
 function tagFileReviewed(sessionId, documentId, options = {}) {
   const existing = queryOne(
@@ -941,10 +990,10 @@ function flagFileQualityIssue(sessionFileId, issues) {
   );
   const current = existing?.quality_issues ? JSON.parse(existing.quality_issues) : [];
   const merged = [.../* @__PURE__ */ new Set([...current, ...issues])];
-  run(
-    `UPDATE session_files SET quality_issues = ? WHERE id = ?`,
-    [JSON.stringify(merged), sessionFileId]
-  );
+  run(`UPDATE session_files SET quality_issues = ? WHERE id = ?`, [
+    JSON.stringify(merged),
+    sessionFileId
+  ]);
 }
 function getSessionFiles(sessionId, options = {}) {
   let sql = "SELECT * FROM session_files WHERE session_id = ?";
@@ -1066,9 +1115,7 @@ function getCoverageStats(sessionId, chunkId) {
 }
 function runMigrations() {
   const database = getDatabase();
-  const columns = queryAll(
-    `PRAGMA table_info(documents)`
-  );
+  const columns = queryAll(`PRAGMA table_info(documents)`);
   const columnNames = new Set(columns.map((c) => c.name));
   const newColumns = [
     { name: "meta_status", type: "TEXT" },
@@ -1094,7 +1141,13 @@ function runMigrations() {
     // Tri-state monitoring columns
     { name: "monitoring_category", type: 'TEXT DEFAULT "unknown"' },
     { name: "needs_review", type: "INTEGER DEFAULT 0" },
-    { name: "reviewed_at", type: "TEXT" }
+    { name: "reviewed_at", type: "TEXT" },
+    // Template system columns (v3)
+    { name: "last_approved_at", type: "TEXT" },
+    { name: "last_modified_at", type: "TEXT" },
+    { name: "is_external", type: "INTEGER DEFAULT 0" },
+    { name: "meta_related", type: "TEXT" },
+    { name: "meta_exception", type: "TEXT" }
   ];
   for (const col of newColumns) {
     if (!columnNames.has(col.name)) {
@@ -1163,22 +1216,29 @@ function runMigrations() {
     )
   `);
   try {
-    database.run(`CREATE INDEX IF NOT EXISTS idx_session_files_session ON session_files(session_id)`);
-    database.run(`CREATE INDEX IF NOT EXISTS idx_session_files_document ON session_files(document_id)`);
+    database.run(
+      `CREATE INDEX IF NOT EXISTS idx_session_files_session ON session_files(session_id)`
+    );
+    database.run(
+      `CREATE INDEX IF NOT EXISTS idx_session_files_document ON session_files(document_id)`
+    );
     database.run(`CREATE INDEX IF NOT EXISTS idx_session_files_chunk ON session_files(chunk_id)`);
-    database.run(`CREATE INDEX IF NOT EXISTS idx_session_files_report ON session_files(report_path)`);
+    database.run(
+      `CREATE INDEX IF NOT EXISTS idx_session_files_report ON session_files(report_path)`
+    );
     database.run(`CREATE INDEX IF NOT EXISTS idx_chunks_session ON chunks(session_id)`);
   } catch {
   }
   saveDatabase();
 }
-var db, dbPath;
+var db, dbPath, transactionDepth;
 var init_connection = __esm({
   "src/db/connection.ts"() {
     "use strict";
     init_config();
     db = null;
     dbPath = "";
+    transactionDepth = 0;
   }
 });
 
@@ -1186,14 +1246,14 @@ var init_connection = __esm({
 import { Command as Command23 } from "commander";
 
 // src/index.ts
-var VERSION = true ? "0.2.6" : "0.0.0-dev";
+var VERSION = true ? "0.2.7" : "0.0.0-dev";
 
 // src/bin/aigile.ts
 init_connection();
 
 // src/commands/init.ts
 import { Command } from "commander";
-import { existsSync as existsSync4, mkdirSync as mkdirSync4, appendFileSync, readFileSync as readFileSync3, writeFileSync as writeFileSync4 } from "fs";
+import { existsSync as existsSync4, mkdirSync as mkdirSync4, appendFileSync, readFileSync as readFileSync4, writeFileSync as writeFileSync4 } from "fs";
 import { resolve, join as join4, relative, basename as basename2 } from "path";
 
 // src/utils/git.ts
@@ -1290,7 +1350,7 @@ function error(message, opts = {}) {
     console.error(`${prefix} ${message}`);
   }
 }
-function warning2(message, opts = {}) {
+function warning(message, opts = {}) {
   if (opts.json) {
     console.log(JSON.stringify({ warning: message }));
   } else {
@@ -1351,747 +1411,88 @@ function header(title, opts = {}) {
   console.log(formatted);
 }
 
-// src/services/template-packs.ts
-import { existsSync as existsSync3, mkdirSync as mkdirSync3, writeFileSync as writeFileSync3 } from "fs";
+// src/services/template-loader.ts
+import { readdirSync, statSync, readFileSync as readFileSync3, existsSync as existsSync3, mkdirSync as mkdirSync3, writeFileSync as writeFileSync3 } from "fs";
 import { join as join3, dirname as dirname2 } from "path";
-function createFrontmatter(title, tldr, modules = []) {
-  return `---
-metadata:
-  status: TEMPLATE
-  version: "1.0"
-  tldr: "${tldr}"
-  title: "${title}"
-  modules: [${modules.map((m) => `"${m}"`).join(", ")}]
-  authors: []
-  dependencies: []
----
-
-`;
-}
-function getFullRepoTemplates() {
-  return [
-    // 00_DOCS hierarchy
-    {
-      path: "00_DOCS/00_vision/01_mission-vision.md",
-      content: createFrontmatter(
-        "Mission & Vision",
-        "Define company mission, vision, values, and elevator pitch",
-        ["vision"]
-      ) + `# Mission & Vision
-
-## Mission Statement
-<!-- Why does this company/product exist? -->
-
-## Vision Statement
-<!-- What future are we creating? -->
-
-## Core Values
-<!-- What principles guide our decisions? -->
-
-## Elevator Pitch
-<!-- One sentence: What do we do? -->
-`
-    },
-    {
-      path: "00_DOCS/01_strategy/01_strategic-analysis.md",
-      content: createFrontmatter(
-        "Strategic Analysis",
-        "SWOT analysis and strategic pillars",
-        ["strategy"]
-      ) + `# Strategic Analysis
-
-## SWOT Analysis
-
-### Strengths
--
-
-### Weaknesses
--
-
-### Opportunities
--
-
-### Threats
--
-
-## Strategic Pillars
-<!-- Key focus areas for the next 1-3 years -->
-
-`
-    },
-    {
-      path: "00_DOCS/02_target-audience/01_personas.md",
-      content: createFrontmatter(
-        "User Personas",
-        "Define ideal customer profile and user personas",
-        ["personas", "ux"]
-      ) + `# User Personas
-
-## Ideal Customer Profile (ICP)
-<!-- Who is our primary customer? -->
-
-## Primary Personas
-
-### Persona 1: [Name]
-- **Role:**
-- **Goals:**
-- **Frustrations:**
-- **Key Tasks:**
-
-`
-    },
-    {
-      path: "00_DOCS/03_finance-legal/01_model.md",
-      content: createFrontmatter(
-        "Business Model",
-        "Revenue model and financial overview",
-        ["finance"]
-      ) + `# Business Model
-
-## Revenue Model
-<!-- How do we make money? -->
-
-## Pricing Strategy
-<!-- How do we price our offerings? -->
-
-## Key Metrics
-<!-- What metrics matter most? -->
-
-`
-    },
-    {
-      path: "00_DOCS/04_raw-inputs/README.md",
-      content: createFrontmatter(
-        "Raw Inputs",
-        "Repository for raw user feedback, interviews, and research data",
-        ["research"]
-      ) + `# Raw Inputs
-
-This directory contains raw, unprocessed input from users, stakeholders, and research.
-
-## Contents
-- User interviews
-- Survey responses
-- Support tickets
-- Feature requests
-- Competitive intelligence
-
-`
-    },
-    {
-      path: "00_DOCS/05_research/README.md",
-      content: createFrontmatter(
-        "Research",
-        "Market research and analysis documents",
-        ["research"]
-      ) + `# Research
-
-This directory contains research and analysis documents.
-
-## Contents
-- Market analysis
-- User research
-- Technical research
-- Competitive analysis
-
-`
-    },
-    {
-      path: "00_DOCS/06_product-specs/01_prd.md",
-      content: createFrontmatter(
-        "Product Requirements Document",
-        "Main PRD template for product features",
-        ["product", "specs"]
-      ) + `# Product Requirements Document (PRD)
-
-## Overview
-<!-- Brief description of the product/feature -->
-
-## Problem Statement
-<!-- What problem are we solving? -->
-
-## Goals & Success Metrics
-<!-- How will we measure success? -->
-
-## User Stories
-<!-- Link to user stories -->
-
-## Requirements
-### Functional Requirements
--
-
-### Non-Functional Requirements
--
-
-## Out of Scope
--
-
-`
-    },
-    {
-      path: "00_DOCS/06_product-specs/epics/README.md",
-      content: createFrontmatter(
-        "Epics Directory",
-        "Contains epic-level product specifications",
-        ["product", "epics"]
-      ) + `# Epics
-
-This directory contains epic-level specifications.
-
-`
-    },
-    {
-      path: "00_DOCS/06_product-specs/stories/README.md",
-      content: createFrontmatter(
-        "User Stories Directory",
-        "Contains user story specifications",
-        ["product", "stories"]
-      ) + `# User Stories
-
-This directory contains user story specifications.
-
-`
-    },
-    {
-      path: "00_DOCS/07_ux-design/00_README.md",
-      content: createFrontmatter(
-        "UX Design",
-        "UX design documentation and journey maps",
-        ["ux"]
-      ) + `# UX Design
-
-## Contents
-- User journeys
-- Wireframes
-- Design system references
-- Interaction patterns
-
-`
-    },
-    {
-      path: "00_DOCS/07_ux-design/journeys/README.md",
-      content: createFrontmatter(
-        "User Journeys",
-        "User journey maps and flow documentation",
-        ["ux", "journeys"]
-      ) + `# User Journeys
-
-This directory contains user journey maps.
-
-`
-    },
-    {
-      path: "00_DOCS/08_go-to-market/01_launch-plan.md",
-      content: createFrontmatter(
-        "Launch Plan",
-        "Go-to-market strategy and launch checklist",
-        ["gtm"]
-      ) + `# Launch Plan
-
-## Launch Goals
--
-
-## Target Audience
--
-
-## Channels
--
-
-## Timeline
--
-
-## Checklist
-- [ ] Marketing materials ready
-- [ ] Documentation complete
-- [ ] Support trained
-- [ ] Analytics configured
-
-`
-    },
-    {
-      path: "00_DOCS/11_people-ops/ai-agents/README.md",
-      content: createFrontmatter(
-        "AI Agents",
-        "AI agent configurations and prompts",
-        ["ai", "agents"]
-      ) + `# AI Agents
-
-This directory contains AI agent configurations and prompts.
-
-`
-    },
-    {
-      path: "00_DOCS/11_people-ops/sops/README.md",
-      content: createFrontmatter(
-        "Standard Operating Procedures",
-        "Team SOPs and process documentation",
-        ["sops"]
-      ) + `# Standard Operating Procedures
-
-This directory contains team SOPs and process documentation.
-
-`
-    },
-    {
-      path: "00_DOCS/12_customer-success/installation.md",
-      content: createFrontmatter(
-        "Installation Guide",
-        "Installation and setup instructions",
-        ["docs", "installation"]
-      ) + `# Installation Guide
-
-## Prerequisites
--
-
-## Installation Steps
-1.
-2.
-3.
-
-## Verification
--
-
-`
-    },
-    {
-      path: "00_DOCS/12_customer-success/quick-start.md",
-      content: createFrontmatter(
-        "Quick Start Guide",
-        "Getting started guide for new users",
-        ["docs", "quickstart"]
-      ) + `# Quick Start Guide
-
-## Overview
-<!-- Brief intro -->
-
-## Step 1: Setup
-<!-- First step -->
-
-## Step 2: First Action
-<!-- Second step -->
-
-## Next Steps
-<!-- What to do next -->
-
-`
-    },
-    {
-      path: "00_DOCS/12_customer-success/troubleshooting.md",
-      content: createFrontmatter(
-        "Troubleshooting Guide",
-        "Common issues and solutions",
-        ["docs", "troubleshooting"]
-      ) + `# Troubleshooting
-
-## Common Issues
-
-### Issue: [Description]
-**Symptoms:**
-**Solution:**
-
-`
-    },
-    {
-      path: "00_DOCS/99_archive/00_README.md",
-      content: createFrontmatter(
-        "Archive",
-        "Archived documents no longer in active use",
-        ["archive"]
-      ) + `# Archive
-
-This directory contains archived documents that are no longer in active use but are kept for reference.
-
-`
-    },
-    // 01_SPECS hierarchy
-    {
-      path: "01_SPECS/00_adr/README.md",
-      content: createFrontmatter(
-        "Architecture Decision Records",
-        "ADRs documenting key technical decisions",
-        ["specs", "adr"]
-      ) + `# Architecture Decision Records (ADRs)
-
-This directory contains ADRs for documenting key technical decisions.
-
-## Template
-Use the template in \`template.md\` for new ADRs.
-
-`
-    },
-    {
-      path: "01_SPECS/01_domain-models/README.md",
-      content: createFrontmatter(
-        "Domain Models",
-        "Domain model specifications",
-        ["specs", "domain"]
-      ) + `# Domain Models
-
-This directory contains domain model specifications.
-
-`
-    },
-    {
-      path: "01_SPECS/02_api-contracts/README.md",
-      content: createFrontmatter(
-        "API Contracts",
-        "API specifications and contracts",
-        ["specs", "api"]
-      ) + `# API Contracts
-
-This directory contains API specifications and contracts.
-
-`
-    },
-    {
-      path: "01_SPECS/03_c4-components/README.md",
-      content: createFrontmatter(
-        "C4 Architecture",
-        "C4 model component diagrams",
-        ["specs", "architecture"]
-      ) + `# C4 Architecture Components
-
-This directory contains C4 model architecture diagrams.
-
-`
-    },
-    {
-      path: "01_SPECS/04_ui-ux-specs/README.md",
-      content: createFrontmatter(
-        "UI/UX Specifications",
-        "UI/UX technical specifications",
-        ["specs", "ux"]
-      ) + `# UI/UX Specifications
-
-This directory contains UI/UX technical specifications.
-
-`
-    },
-    {
-      path: "01_SPECS/05_infrastructure/README.md",
-      content: createFrontmatter(
-        "Infrastructure",
-        "Infrastructure and deployment specifications",
-        ["specs", "infra"]
-      ) + `# Infrastructure
-
-This directory contains infrastructure and deployment specifications.
-
-`
-    },
-    // 02_FEATURES hierarchy
-    {
-      path: "02_FEATURES/00_smoke-tests/README.md",
-      content: createFrontmatter(
-        "Smoke Tests",
-        "Critical path smoke test scenarios",
-        ["features", "tests"]
-      ) + `# Smoke Tests
-
-This directory contains smoke test feature files for critical paths.
-
-`
-    },
-    {
-      path: "02_FEATURES/01_epics/README.md",
-      content: createFrontmatter(
-        "Epic Features",
-        "BDD feature files organized by epic",
-        ["features", "epics"]
-      ) + `# Epic Features
-
-This directory contains BDD feature files organized by epic.
-
-`
-    },
-    {
-      path: "02_FEATURES/02_end-to-end/README.md",
-      content: createFrontmatter(
-        "End-to-End Features",
-        "End-to-end scenario feature files",
-        ["features", "e2e"]
-      ) + `# End-to-End Features
-
-This directory contains end-to-end scenario feature files.
-
-`
-    },
-    {
-      path: "02_FEATURES/03_nfr/README.md",
-      content: createFrontmatter(
-        "Non-Functional Requirements",
-        "NFR feature files (performance, security, etc.)",
-        ["features", "nfr"]
-      ) + `# Non-Functional Requirements
-
-This directory contains NFR feature files:
-- Performance
-- Security
-- Scalability
-- Accessibility
-
-`
-    },
-    // 03_TESTING_INFRA hierarchy
-    {
-      path: "03_TESTING_INFRA/00_governance/README.md",
-      content: createFrontmatter(
-        "Test Governance",
-        "Testing standards and policies",
-        ["testing", "governance"]
-      ) + `# Test Governance
-
-This directory contains testing standards and policies.
-
-`
-    },
-    {
-      path: "03_TESTING_INFRA/01_unit-layer/README.md",
-      content: createFrontmatter(
-        "Unit Testing Layer",
-        "Unit test infrastructure and guides",
-        ["testing", "unit"]
-      ) + `# Unit Testing Layer
-
-This directory contains unit test infrastructure.
-
-`
-    },
-    {
-      path: "03_TESTING_INFRA/02_integration-layer/README.md",
-      content: createFrontmatter(
-        "Integration Testing Layer",
-        "Integration test infrastructure and guides",
-        ["testing", "integration"]
-      ) + `# Integration Testing Layer
-
-This directory contains integration test infrastructure.
-
-`
-    },
-    {
-      path: "03_TESTING_INFRA/03_e2e-layer/README.md",
-      content: createFrontmatter(
-        "E2E Testing Layer",
-        "End-to-end test infrastructure and guides",
-        ["testing", "e2e"]
-      ) + `# E2E Testing Layer
-
-This directory contains E2E test infrastructure.
-
-`
-    },
-    {
-      path: "03_TESTING_INFRA/04_manual-qa-layer/README.md",
-      content: createFrontmatter(
-        "Manual QA Layer",
-        "Manual QA procedures and checklists",
-        ["testing", "qa"]
-      ) + `# Manual QA Layer
-
-This directory contains manual QA procedures and checklists.
-
-`
-    },
-    {
-      path: "03_TESTING_INFRA/qa/README.md",
-      content: createFrontmatter(
-        "QA Documentation",
-        "QA procedures and documentation",
-        ["testing", "qa"]
-      ) + `# QA Documentation
-
-This directory contains QA procedures and documentation.
-
-`
-    },
-    {
-      path: "03_TESTING_INFRA/reports/README.md",
-      content: createFrontmatter(
-        "Test Reports",
-        "Test execution reports",
-        ["testing", "reports"]
-      ) + `# Test Reports
-
-This directory contains test execution reports.
-
-`
-    }
-  ];
+import { fileURLToPath } from "url";
+var __filename = fileURLToPath(import.meta.url);
+var __dirname = dirname2(__filename);
+function getTemplateDir(profile) {
+  const isDev = process.env.NODE_ENV === "development" || !process.pkg;
+  let baseDir;
+  if (isDev) {
+    baseDir = join3(__dirname, "..", "..", "artifacts", "templates");
+  } else {
+    baseDir = join3(__dirname, "..", "artifacts", "templates");
+  }
+  return join3(baseDir, profile);
 }
-function getSubrepoTemplates() {
-  return getFullRepoTemplates();
+function loadTemplates(profile) {
+  const templateDir = getTemplateDir(profile);
+  if (!existsSync3(templateDir)) {
+    throw new Error(`Template directory not found: ${templateDir}`);
+  }
+  return recursiveReadTemplates(templateDir, "");
 }
-function getModuleTemplates(moduleName) {
-  return [
-    {
-      path: "docs/01_module-overview.md",
-      content: createFrontmatter(
-        `${moduleName} Overview`,
-        `Overview documentation for ${moduleName} module`,
-        [moduleName]
-      ) + `# ${moduleName} Module Overview
-
-## Purpose
-<!-- What does this module do? -->
-
-## Key Concepts
-<!-- Core concepts and terminology -->
-
-## Dependencies
-<!-- What does this module depend on? -->
-
-## API
-<!-- Public API surface -->
-
-`
-    },
-    {
-      path: "docs/02_mini-prd.md",
-      content: createFrontmatter(
-        `${moduleName} Requirements`,
-        `Module-level requirements for ${moduleName}`,
-        [moduleName, "specs"]
-      ) + `# ${moduleName} Module Requirements
-
-## Goals
-<!-- What should this module achieve? -->
-
-## Requirements
-### Functional
--
-
-### Non-Functional
--
-
-## Out of Scope
--
-
-`
-    },
-    {
-      path: "specs/01_spec-template.md",
-      content: createFrontmatter(
-        `${moduleName} Spec Template`,
-        `Specification template for ${moduleName}`,
-        [moduleName, "specs"]
-      ) + `# ${moduleName} Specification
-
-## Overview
-<!-- Brief description -->
-
-## Design
-<!-- Technical design -->
-
-## Implementation Notes
-<!-- Key implementation details -->
-
-`
-    },
-    {
-      path: "features/01_happy-path.feature",
-      content: `Feature: ${moduleName} Happy Path
-  As a user
-  I want to use ${moduleName}
-  So that I can achieve my goals
-
-  Scenario: Basic usage
-    Given I have configured ${moduleName}
-    When I perform the main action
-    Then I should see the expected result
-`
-    },
-    {
-      path: "features/02_edge-cases.feature",
-      content: `Feature: ${moduleName} Edge Cases
-  As a user
-  I want ${moduleName} to handle edge cases gracefully
-  So that I don't encounter errors
-
-  Scenario: Empty input
-    Given I have configured ${moduleName}
-    When I provide empty input
-    Then I should see a helpful error message
-`
+function recursiveReadTemplates(baseDir, relativePath) {
+  const fullPath = join3(baseDir, relativePath);
+  if (!existsSync3(fullPath)) {
+    return [];
+  }
+  const entries = readdirSync(fullPath);
+  const files = [];
+  for (const entry of entries) {
+    const entryPath = join3(fullPath, entry);
+    const entryRelative = relativePath ? join3(relativePath, entry) : entry;
+    try {
+      const stat = statSync(entryPath);
+      if (stat.isDirectory()) {
+        files.push(...recursiveReadTemplates(baseDir, entryRelative));
+      } else if (stat.isFile()) {
+        const content = readFileSync3(entryPath, "utf-8");
+        files.push({
+          relativePath: entryRelative,
+          content
+        });
+      }
+    } catch (err) {
+      console.warn(`Warning: Could not read ${entryPath}: ${err}`);
     }
-  ];
-}
-function getTemplatesForProfile(profile, moduleName) {
-  switch (profile) {
-    case "full-repo":
-      return getFullRepoTemplates();
-    case "subrepo":
-      return getSubrepoTemplates();
-    case "module":
-      return getModuleTemplates(moduleName ?? "module");
-    default:
-      return [];
   }
+  return files;
 }
 function writeTemplates(targetDir, templates) {
   let written = 0;
   let skipped = 0;
+  const errors = [];
   for (const template of templates) {
-    const fullPath = join3(targetDir, template.path);
-    const dir = dirname2(fullPath);
-    if (!existsSync3(dir)) {
-      mkdirSync3(dir, { recursive: true });
+    const fullPath = join3(targetDir, template.relativePath);
+    if (existsSync3(fullPath)) {
+      skipped++;
+      continue;
     }
-    if (!existsSync3(fullPath)) {
+    try {
+      const dir = dirname2(fullPath);
+      if (!existsSync3(dir)) {
+        mkdirSync3(dir, { recursive: true });
+      }
       writeFileSync3(fullPath, template.content, "utf-8");
       written++;
-    } else {
-      skipped++;
+    } catch (err) {
+      errors.push({
+        path: template.relativePath,
+        error: err instanceof Error ? err.message : String(err)
+      });
     }
   }
-  return { written, skipped };
-}
-function generateConfigYaml(config, projectKey, projectName) {
-  let yaml = `# AIGILE Project Configuration
-# Auto-generated by aigile init
-
-db:
-  mode: ${config.db.mode}
-  path: ${config.db.path}
-
-profile: ${config.profile}
-repo_root: ${config.repo_root}
-`;
-  if (config.parent_repo_root) {
-    yaml += `parent_repo_root: ${config.parent_repo_root}
-`;
-  }
-  if (config.module) {
-    yaml += `
-module:
-  name: ${config.module.name}
-  kind: ${config.module.kind}
-  path: ${config.module.path}
-`;
-  }
-  yaml += `
-project:
-  key: ${projectKey}
-  name: ${projectName}
-
-sync:
-  enabled: true
-  patterns:
-    - "**/*.md"
-    - "**/*.feature"
-    - "**/*.yaml"
-    - "**/*.yml"
-  ignore:
-    - node_modules
-    - dist
-    - .git
-    - coverage
-`;
-  return yaml;
+  return { written, skipped, errors };
 }
 
 // src/commands/init.ts
-var initCommand = new Command("init").description("Initialize AIGILE in current or specified directory").argument("[path]", "Directory path (defaults to current directory)").option("-k, --key <key>", "Project key (auto-generated if not specified)").option("-n, --name <name>", "Project name (auto-detected if not specified)").option("-p, --profile <profile>", "Init profile: full-repo, subrepo, module").option("--db-mode <mode>", "Database mode: local, shared (default based on profile)").option("--module-kind <kind>", "Module kind: library, service, ui, cli, other (for module profile)").option("--skip-templates", "Skip template file creation").option("-f, --force", "Reinitialize existing project").action(async (pathArg, options) => {
+var initCommand = new Command("init").description("Initialize AIGILE in current or specified directory").argument("[path]", "Directory path (defaults to current directory)").option("-k, --key <key>", "Project key (auto-generated if not specified)").option("-n, --name <name>", "Project name (auto-detected if not specified)").option("-p, --profile <profile>", "Init profile: full-repo, minor-project, module").option("--db-mode <mode>", "Database mode: local, shared (default based on profile)").option(
+  "--module-kind <kind>",
+  "Module kind: library, service, ui, cli, other (for module profile)"
+).option("--skip-templates", "Skip template file creation").option("-f, --force", "Reinitialize existing project").action(async (pathArg, options) => {
   const opts = getOutputOptions(initCommand);
   const targetPath = resolve(pathArg ?? process.cwd());
   try {
@@ -2118,7 +1519,7 @@ function detectGitContext(targetPath) {
     relativePath
   };
 }
-var VALID_PROFILES = ["full-repo", "subrepo", "module"];
+var VALID_PROFILES = ["full-repo", "minor-project", "module"];
 function determineProfile(context, options, opts) {
   if (options.profile) {
     if (!VALID_PROFILES.includes(options.profile)) {
@@ -2129,8 +1530,8 @@ function determineProfile(context, options, opts) {
     return options.profile;
   }
   if (context.isSubmodule) {
-    info("Detected git submodule - using subrepo profile", opts);
-    return "subrepo";
+    info("Detected git submodule - using minor-project profile", opts);
+    return "minor-project";
   }
   if (context.isSubdirectory) {
     const parentAigile = join4(context.gitRoot, ".aigile");
@@ -2153,7 +1554,7 @@ function determineDbMode(profile, context, options) {
   switch (profile) {
     case "full-repo":
       return { mode: "local", path: ".aigile/aigile.db" };
-    case "subrepo":
+    case "minor-project":
       return { mode: "local", path: ".aigile/aigile.db" };
     case "module":
       const parentDbPath = findParentDb(context);
@@ -2176,6 +1577,33 @@ function findParentDb(context) {
   }
   return ".aigile/aigile.db";
 }
+function generateConfigYaml(config, projectKey, projectName) {
+  const lines = ["# AIGILE Project Configuration", ""];
+  lines.push("project:");
+  lines.push(`  key: "${projectKey}"`);
+  lines.push(`  name: "${projectName}"`);
+  lines.push("");
+  lines.push("db:");
+  lines.push(`  mode: ${config.db.mode}`);
+  lines.push(`  path: ${config.db.path}`);
+  lines.push("");
+  lines.push(`profile: ${config.profile}`);
+  lines.push("");
+  lines.push(`repo_root: ${config.repo_root}`);
+  if (config.module) {
+    lines.push("");
+    lines.push("module:");
+    lines.push(`  name: ${config.module.name}`);
+    lines.push(`  kind: ${config.module.kind}`);
+    lines.push(`  path: ${config.module.path}`);
+  }
+  if (config.parent_repo_root) {
+    lines.push("");
+    lines.push(`parent_repo_root: ${config.parent_repo_root}`);
+  }
+  lines.push("");
+  return lines.join("\n");
+}
 async function initProject(targetPath, options, opts) {
   if (!isGitRepo(targetPath)) {
     throw new Error('AIGILE requires a git repository. Run "git init" first.');
@@ -2225,35 +1653,47 @@ async function initProject(targetPath, options, opts) {
       kind: options.moduleKind ?? "other",
       path: context.relativePath
     };
-    aigileConfig.parent_repo_root = "../".repeat(context.relativePath.split("/").filter((p) => p).length);
+    aigileConfig.parent_repo_root = "../".repeat(
+      context.relativePath.split("/").filter((p) => p).length
+    );
   }
-  if (profile === "subrepo" && context.superprojectRoot) {
+  if (profile === "minor-project" && context.superprojectRoot) {
     aigileConfig.parent_repo_root = "..";
   }
   const configYaml = generateConfigYaml(aigileConfig, projectKey, projectName);
   writeFileSync4(join4(aigileDir, "config.yaml"), configYaml, "utf-8");
-  let templatesResult = { written: 0, skipped: 0 };
+  let templatesResult = { written: 0, skipped: 0, errors: [] };
   if (!options.skipTemplates) {
-    const templates = getTemplatesForProfile(profile, moduleName);
-    templatesResult = writeTemplates(aigileDir, templates);
+    try {
+      const templates = loadTemplates(profile);
+      templatesResult = writeTemplates(targetPath, templates);
+    } catch (err) {
+      warning(
+        `Could not load templates: ${err instanceof Error ? err.message : String(err)}`,
+        opts
+      );
+    }
   }
   if (dbConfig.mode === "local") {
     registerProject(targetPath, (projectId) => {
-      const existingProject = queryOne(
-        "SELECT id FROM projects WHERE path = ?",
-        [targetPath]
-      );
+      const existingProject = queryOne("SELECT id FROM projects WHERE path = ?", [
+        targetPath
+      ]);
       const id = existingProject?.id ?? generateId();
       if (existingProject) {
-        run(
-          `UPDATE projects SET key = ?, name = ?, updated_at = datetime('now') WHERE id = ?`,
-          [projectKey, projectName, id]
-        );
+        run(`UPDATE projects SET key = ?, name = ?, updated_at = datetime('now') WHERE id = ?`, [
+          projectKey,
+          projectName,
+          id
+        ]);
       } else {
-        run(
-          `INSERT INTO projects (id, key, name, path, is_default) VALUES (?, ?, ?, ?, ?)`,
-          [id, projectKey, projectName, targetPath, 0]
-        );
+        run(`INSERT INTO projects (id, key, name, path, is_default) VALUES (?, ?, ?, ?, ?)`, [
+          id,
+          projectKey,
+          projectName,
+          targetPath,
+          0
+        ]);
       }
       const defaultProject = queryOne(
         "SELECT id FROM projects WHERE is_default = 1",
@@ -2267,17 +1707,19 @@ async function initProject(targetPath, options, opts) {
   }
   updateGitignore(targetPath, opts);
   if (opts.json) {
-    console.log(JSON.stringify({
-      success: true,
-      project: {
-        key: projectKey,
-        name: projectName,
-        path: targetPath,
-        profile,
-        dbMode: dbConfig.mode
-      },
-      templates: templatesResult
-    }));
+    console.log(
+      JSON.stringify({
+        success: true,
+        project: {
+          key: projectKey,
+          name: projectName,
+          path: targetPath,
+          profile,
+          dbMode: dbConfig.mode
+        },
+        templates: templatesResult
+      })
+    );
   } else {
     blank();
     success(`AIGILE initialized with ${profile} profile`, opts);
@@ -2293,11 +1735,14 @@ async function initProject(targetPath, options, opts) {
       header("Templates:", opts);
       console.log(`  Written:  ${templatesResult.written} files`);
       console.log(`  Skipped:  ${templatesResult.skipped} files (already exist)`);
+      if (templatesResult.errors.length > 0) {
+        console.log(`  Errors:   ${templatesResult.errors.length} files`);
+      }
     }
     blank();
     header("Next steps:", opts);
-    if (profile === "full-repo" || profile === "subrepo") {
-      console.log("  1. Fill in 00_DOCS/00_vision/01_mission-vision.md");
+    if (profile === "full-repo" || profile === "minor-project") {
+      console.log("  1. Fill in 00_DOCS/01_vision-foundations/01_mission-vision-values.md");
       console.log('  2. Run "aigile sync scan" to index your files');
       console.log('  3. Run "aigile daemon install && aigile daemon start" for auto-sync');
     } else {
@@ -2317,7 +1762,7 @@ function updateGitignore(repoPath, opts) {
     info('No .gitignore found. Consider adding ".aigile/" to ignore local config.', opts);
     return;
   }
-  const content = readFileSync3(gitignorePath, "utf-8");
+  const content = readFileSync4(gitignorePath, "utf-8");
   const lines = content.split("\n");
   const hasPattern = lines.some((line) => {
     const trimmed = line.trim();
@@ -2399,7 +1844,7 @@ projectCommand.command("list").alias("ls").description("List all registered proj
   console.log("  \u2713 = valid path, \u2717 = missing/invalid path");
   if (invalidCount > 0) {
     blank();
-    warning2(`${invalidCount} project(s) have invalid paths. Run "aigile project cleanup" to remove.`, opts);
+    warning(`${invalidCount} project(s) have invalid paths. Run "aigile project cleanup" to remove.`, opts);
   }
 });
 projectCommand.command("show").argument("[key]", "Project key (uses default if not specified)").description("Show project details").action((key) => {
@@ -2808,7 +2253,7 @@ epicCommand.command("delete").alias("rm").argument("<key>", "Epic key").option("
            (SELECT id FROM user_stories WHERE epic_id = ?)`,
         [epic.id]
       );
-      warning2(
+      warning(
         `Deleting ${childCount.count} child story(s) and ${taskCount?.count || 0} task(s)`,
         opts
       );
@@ -2818,7 +2263,7 @@ epicCommand.command("delete").alias("rm").argument("<key>", "Epic key").option("
       );
       run("DELETE FROM user_stories WHERE epic_id = ?", [epic.id]);
     } else {
-      warning2(`Orphaning ${childCount.count} child story(s)`, opts);
+      warning(`Orphaning ${childCount.count} child story(s)`, opts);
       run("UPDATE user_stories SET epic_id = NULL WHERE epic_id = ?", [epic.id]);
     }
   }
@@ -3017,10 +2462,10 @@ storyCommand.command("delete").alias("rm").argument("<key>", "Story key").option
       process.exit(1);
     }
     if (options.cascade) {
-      warning2(`Deleting ${childCount.count} child task(s)`, opts);
+      warning(`Deleting ${childCount.count} child task(s)`, opts);
       run("DELETE FROM tasks WHERE story_id = ?", [story.id]);
     } else {
-      warning2(`Orphaning ${childCount.count} child task(s)`, opts);
+      warning(`Orphaning ${childCount.count} child task(s)`, opts);
       run("UPDATE tasks SET story_id = NULL WHERE story_id = ?", [story.id]);
     }
   }
@@ -3983,11 +3428,11 @@ init_config();
 // src/services/file-scanner.ts
 init_connection();
 import { createHash } from "crypto";
-import { readFileSync as readFileSync5, statSync, readdirSync, existsSync as existsSync6 } from "fs";
+import { readFileSync as readFileSync6, statSync as statSync2, readdirSync as readdirSync2, existsSync as existsSync6 } from "fs";
 import { join as join6, relative as relative2, extname } from "path";
 
 // src/services/frontmatter-parser.ts
-import { readFileSync as readFileSync4 } from "fs";
+import { readFileSync as readFileSync5 } from "fs";
 import { parse as parseYaml2 } from "yaml";
 var FRONTMATTER_REGEX = /^---\r?\n([\s\S]*?)\r?\n---\r?\n?/;
 function extractFrontmatter(content) {
@@ -4009,9 +3454,11 @@ function extractFrontmatter(content) {
         tldr: data2?.tldr,
         modules: data2?.modules,
         dependencies: data2?.dependencies,
+        related: data2?.related,
         code_refs: data2?.code_refs,
         authors: data2?.authors,
-        title: data2?.title
+        title: data2?.title,
+        exception: data2?.exception
       };
     }
     if (metadata.modules && !Array.isArray(metadata.modules)) {
@@ -4020,6 +3467,9 @@ function extractFrontmatter(content) {
     if (metadata.dependencies && !Array.isArray(metadata.dependencies)) {
       metadata.dependencies = [String(metadata.dependencies)];
     }
+    if (metadata.related && !Array.isArray(metadata.related)) {
+      metadata.related = [String(metadata.related)];
+    }
     if (metadata.code_refs && !Array.isArray(metadata.code_refs)) {
       metadata.code_refs = [String(metadata.code_refs)];
     }
@@ -4039,7 +3489,7 @@ function extractFrontmatter(content) {
 }
 function parseFrontmatterFromFile(filePath) {
   try {
-    const content = readFileSync4(filePath, "utf-8");
+    const content = readFileSync5(filePath, "utf-8");
     return extractFrontmatter(content);
   } catch {
     return null;
@@ -4068,9 +3518,15 @@ function serializeMetadata(metadata) {
   if (metadata.dependencies && metadata.dependencies.length > 0) {
     lines.push(`  dependencies: [${metadata.dependencies.join(", ")}]`);
   }
+  if (metadata.related && metadata.related.length > 0) {
+    lines.push(`  related: [${metadata.related.join(", ")}]`);
+  }
   if (metadata.code_refs && metadata.code_refs.length > 0) {
     lines.push(`  code_refs: [${metadata.code_refs.join(", ")}]`);
   }
+  if (metadata.exception) {
+    lines.push(`  exception: "${metadata.exception.replace(/"/g, '\\"')}"`);
+  }
   lines.push("---");
   return lines.join("\n");
 }
@@ -4092,22 +3548,18 @@ function updateFrontmatterContent(content, updates) {
     ...updates
   };
   if (updates.dependencies && existing.metadata.dependencies) {
-    merged.dependencies = [.../* @__PURE__ */ new Set([
-      ...existing.metadata.dependencies,
-      ...updates.dependencies
-    ])];
+    merged.dependencies = [
+      .../* @__PURE__ */ new Set([...existing.metadata.dependencies, ...updates.dependencies])
+    ];
   }
   if (updates.modules && existing.metadata.modules) {
-    merged.modules = [.../* @__PURE__ */ new Set([
-      ...existing.metadata.modules,
-      ...updates.modules
-    ])];
+    merged.modules = [.../* @__PURE__ */ new Set([...existing.metadata.modules, ...updates.modules])];
+  }
+  if (updates.related && existing.metadata.related) {
+    merged.related = [.../* @__PURE__ */ new Set([...existing.metadata.related, ...updates.related])];
   }
   if (updates.code_refs && existing.metadata.code_refs) {
-    merged.code_refs = [.../* @__PURE__ */ new Set([
-      ...existing.metadata.code_refs,
-      ...updates.code_refs
-    ])];
+    merged.code_refs = [.../* @__PURE__ */ new Set([...existing.metadata.code_refs, ...updates.code_refs])];
   }
   const newFrontmatter = serializeMetadata(merged);
   return content.replace(FRONTMATTER_REGEX, newFrontmatter + "\n\n");
@@ -4118,7 +3570,7 @@ init_monitoring_patterns();
 init_config();
 import picomatch from "picomatch";
 function computeFileHash(filePath) {
-  const content = readFileSync5(filePath);
+  const content = readFileSync6(filePath);
   return createHash("sha256").update(content).digest("hex");
 }
 var FileClassifier = class {
@@ -4156,7 +3608,7 @@ function collectFiles(dir, rootDir, classifier, trackUnknown, files = []) {
   if (!existsSync6(dir)) {
     return files;
   }
-  const entries = readdirSync(dir, { withFileTypes: true });
+  const entries = readdirSync2(dir, { withFileTypes: true });
   for (const entry of entries) {
     const fullPath = join6(dir, entry.name);
     const relativePath = relative2(rootDir, fullPath);
@@ -4178,7 +3630,7 @@ function collectFiles(dir, rootDir, classifier, trackUnknown, files = []) {
         continue;
       }
       try {
-        const stats = statSync(fullPath);
+        const stats = statSync2(fullPath);
         const ext = extname(entry.name).toLowerCase().slice(1);
         const isBinary = isBinaryExtension(ext);
         const shouldComputeHash = category === "allow" || !isBinary && stats.size < 10 * 1024 * 1024;
@@ -4372,82 +3824,16 @@ function getDocuments(projectId, status) {
     params.push(status);
   }
   query += " ORDER BY path";
-  return queryAll(query, params);
-}
-function getDocumentsByMetaStatus(projectId, metaStatus) {
-  return queryAll(
-    `SELECT id, path, filename, extension, status, size_bytes, last_scanned_at,
-            has_frontmatter, meta_status, meta_version, meta_tldr, meta_title,
-            meta_modules, meta_dependencies, meta_code_refs, meta_authors
-     FROM documents
-     WHERE project_id = ? AND meta_status = ? AND status != 'deleted'
-     ORDER BY path`,
-    [projectId, metaStatus]
-  );
-}
-function getDocumentsByModule(projectId, module) {
-  return queryAll(
-    `SELECT id, path, filename, extension, status, size_bytes, last_scanned_at,
-            has_frontmatter, meta_status, meta_version, meta_tldr, meta_title,
-            meta_modules, meta_dependencies, meta_code_refs, meta_authors
-     FROM documents
-     WHERE project_id = ? AND meta_modules LIKE ? AND status != 'deleted'
-     ORDER BY path`,
-    [projectId, `%"${module}"%`]
-  );
-}
-function getDocumentsWithFrontmatter(projectId) {
-  return queryAll(
-    `SELECT id, path, filename, extension, status, size_bytes, last_scanned_at,
-            has_frontmatter, meta_status, meta_version, meta_tldr, meta_title,
-            meta_modules, meta_dependencies, meta_code_refs, meta_authors
-     FROM documents
-     WHERE project_id = ? AND has_frontmatter = 1 AND status != 'deleted'
-     ORDER BY path`,
-    [projectId]
-  );
-}
-function getDocumentsWithoutFrontmatter(projectId) {
-  return queryAll(
-    `SELECT id, path, filename, extension, status, size_bytes, last_scanned_at,
-            has_frontmatter, meta_status, meta_version, meta_tldr, meta_title,
-            meta_modules, meta_dependencies, meta_code_refs, meta_authors
-     FROM documents
-     WHERE project_id = ? AND (has_frontmatter = 0 OR has_frontmatter IS NULL) AND status != 'deleted'
-     ORDER BY path`,
-    [projectId]
-  );
-}
-function getDocumentByPath(projectId, filePath) {
-  return queryOne(
-    `SELECT id, path, filename, extension, status, size_bytes, last_scanned_at,
-            has_frontmatter, meta_status, meta_version, meta_tldr, meta_title,
-            meta_modules, meta_dependencies, meta_code_refs, meta_authors
-     FROM documents
-     WHERE project_id = ? AND path = ?`,
-    [projectId, filePath]
-  );
-}
-function getTemplateDocuments(projectId) {
-  return queryAll(
-    `SELECT id, path, filename, extension, status, size_bytes, last_scanned_at,
-            has_frontmatter, meta_status, meta_version, meta_tldr, meta_title,
-            meta_modules, meta_dependencies, meta_code_refs, meta_authors
-     FROM documents
-     WHERE project_id = ? AND meta_status = 'TEMPLATE' AND status != 'deleted'
-     ORDER BY path`,
-    [projectId]
-  );
+  return queryAll(query, params);
 }
-function searchDocumentsByTldr(projectId, searchTerm) {
-  return queryAll(
+function getDocumentByPath(projectId, filePath) {
+  return queryOne(
     `SELECT id, path, filename, extension, status, size_bytes, last_scanned_at,
             has_frontmatter, meta_status, meta_version, meta_tldr, meta_title,
             meta_modules, meta_dependencies, meta_code_refs, meta_authors
      FROM documents
-     WHERE project_id = ? AND meta_tldr LIKE ? AND status != 'deleted'
-     ORDER BY path`,
-    [projectId, `%${searchTerm}%`]
+     WHERE project_id = ? AND path = ?`,
+    [projectId, filePath]
   );
 }
 function getUnanalyzedDocuments(projectId, limit, offset) {
@@ -4673,7 +4059,7 @@ function trackShadowFile(projectId, projectPath, filePath) {
     return getDocumentWithAnalysis(projectId, filePath) ?? null;
   }
   try {
-    const stats = statSync(fullPath);
+    const stats = statSync2(fullPath);
     const hash = computeFileHash(fullPath);
     const filename = filePath.split("/").pop() ?? filePath;
     const ext = extname(filename).slice(1);
@@ -4694,11 +4080,11 @@ function trackShadowFile(projectId, projectPath, filePath) {
 
 // src/services/comment-parser.ts
 init_connection();
-import { readFileSync as readFileSync6 } from "fs";
+import { readFileSync as readFileSync7 } from "fs";
 var USER_COMMENT_PATTERN = /\[\[!\s*([\s\S]*?)\s*\]\]/g;
 var AI_COMMENT_PATTERN = /\[\{!\s*([\s\S]*?)\s*\}]/g;
 function parseComments(filePath) {
-  const content = readFileSync6(filePath, "utf-8");
+  const content = readFileSync7(filePath, "utf-8");
   const lines = content.split("\n");
   const comments = [];
   const positionToLine = [];
@@ -5059,10 +4445,9 @@ function startSession(projectId, name) {
     [projectId, "active"]
   );
   if (existing) {
-    run(
-      `UPDATE sessions SET status = 'abandoned', ended_at = datetime('now') WHERE id = ?`,
-      [existing.id]
-    );
+    run(`UPDATE sessions SET status = 'abandoned', ended_at = datetime('now') WHERE id = ?`, [
+      existing.id
+    ]);
   }
   const sessionId = generateId();
   const now = (/* @__PURE__ */ new Date()).toISOString();
@@ -5086,20 +4471,22 @@ function startSession(projectId, name) {
 }
 function endSession(projectId, summary) {
   const session = queryOne(
-    "SELECT id, started_at, entities_modified, files_modified FROM sessions WHERE project_id = ? AND status = ?",
+    "SELECT id, name, started_at, entities_modified, files_modified FROM sessions WHERE project_id = ? AND status = ?",
     [projectId, "active"]
   );
   if (!session) {
     return null;
   }
   const now = (/* @__PURE__ */ new Date()).toISOString();
-  run(
-    `UPDATE sessions SET status = 'completed', ended_at = ?, summary = ? WHERE id = ?`,
-    [now, summary ?? null, session.id]
-  );
+  run(`UPDATE sessions SET status = 'completed', ended_at = ?, summary = ? WHERE id = ?`, [
+    now,
+    summary ?? null,
+    session.id
+  ]);
   return {
     id: session.id,
     projectId,
+    name: session.name,
     startedAt: session.started_at,
     endedAt: now,
     summary: summary ?? null,
@@ -5109,16 +4496,14 @@ function endSession(projectId, summary) {
   };
 }
 function getActiveSession(projectId) {
-  const session = queryOne(
-    "SELECT * FROM sessions WHERE project_id = ? AND status = ?",
-    [projectId, "active"]
-  );
+  const session = queryOne("SELECT * FROM sessions WHERE project_id = ? AND status = ?", [projectId, "active"]);
   if (!session) {
     return null;
   }
   return {
     id: session.id,
     projectId: session.project_id,
+    name: session.name,
     startedAt: session.started_at,
     endedAt: session.ended_at,
     summary: session.summary,
@@ -5128,10 +4513,7 @@ function getActiveSession(projectId) {
   };
 }
 function getSessionByName(projectId, name) {
-  const session = queryOne(
-    "SELECT * FROM sessions WHERE project_id = ? AND name = ?",
-    [projectId, name]
-  );
+  const session = queryOne("SELECT * FROM sessions WHERE project_id = ? AND name = ?", [projectId, name]);
   if (!session) {
     return null;
   }
@@ -5148,10 +4530,7 @@ function getSessionByName(projectId, name) {
   };
 }
 function resumeSession(projectId, sessionId) {
-  const session = queryOne(
-    "SELECT * FROM sessions WHERE id = ? AND project_id = ?",
-    [sessionId, projectId]
-  );
+  const session = queryOne("SELECT * FROM sessions WHERE id = ? AND project_id = ?", [sessionId, projectId]);
   if (!session) {
     return null;
   }
@@ -5163,15 +4542,11 @@ function resumeSession(projectId, sessionId) {
     [projectId, "active", sessionId]
   );
   if (existing) {
-    run(
-      `UPDATE sessions SET status = 'abandoned', ended_at = datetime('now') WHERE id = ?`,
-      [existing.id]
-    );
+    run(`UPDATE sessions SET status = 'abandoned', ended_at = datetime('now') WHERE id = ?`, [
+      existing.id
+    ]);
   }
-  run(
-    `UPDATE sessions SET status = 'active', ended_at = NULL WHERE id = ?`,
-    [sessionId]
-  );
+  run(`UPDATE sessions SET status = 'active', ended_at = NULL WHERE id = ?`, [sessionId]);
   return {
     id: session.id,
     projectId: session.project_id,
@@ -5249,6 +4624,7 @@ function getSession(sessionId) {
   return {
     id: session.id,
     projectId: session.project_id,
+    name: session.name,
     startedAt: session.started_at,
     endedAt: session.ended_at,
     summary: session.summary,
@@ -8419,321 +7795,863 @@ uxJourneyCommand.command("delete").alias("rm").argument("<key>", "Journey key").
 // src/commands/doc.ts
 init_connection();
 import { Command as Command19 } from "commander";
-import { readFileSync as readFileSync7, writeFileSync as writeFileSync5 } from "fs";
-import { join as join8 } from "path";
-init_config();
-var docCommand = new Command19("doc").description("Document management and frontmatter operations");
-function getProjectId(opts) {
-  const projectRoot = findProjectRoot();
-  if (!projectRoot) {
-    error('Not in an AIGILE project. Run "aigile init" first.', opts);
-    return null;
+import { existsSync as existsSync7 } from "fs";
+import { resolve as resolve3, relative as relative4 } from "path";
+
+// src/services/dependency-graph.ts
+init_connection();
+import { resolve as resolve2, relative as relative3, dirname as dirname3 } from "path";
+function buildDependencyGraph(projectId) {
+  const docs = queryAll(
+    `SELECT id, path, meta_status, last_approved_at, last_modified_at, meta_dependencies 
+     FROM documents 
+     WHERE project_id = ?`,
+    [projectId]
+  );
+  const graph = /* @__PURE__ */ new Map();
+  for (const doc of docs) {
+    const dependencies = doc.meta_dependencies ? JSON.parse(doc.meta_dependencies) : [];
+    graph.set(doc.path, {
+      id: doc.id,
+      path: doc.path,
+      status: doc.meta_status || "UNKNOWN",
+      lastApprovedAt: doc.last_approved_at || void 0,
+      lastModifiedAt: doc.last_modified_at || void 0,
+      dependencies,
+      dependents: []
+    });
   }
-  const config = loadProjectConfig(projectRoot);
-  if (!config) {
-    error("Could not load project config.", opts);
-    return null;
+  for (const [path, node] of graph.entries()) {
+    for (const depPath of node.dependencies) {
+      const absoluteDep = resolveDocPath(path, depPath);
+      const depNode = graph.get(absoluteDep);
+      if (depNode) {
+        depNode.dependents.push(path);
+      }
+    }
   }
-  const project = queryOne("SELECT id FROM projects WHERE key = ?", [config.project.key]);
-  if (!project) {
-    error(`Project "${config.project.key}" not found in database.`, opts);
-    return null;
+  return graph;
+}
+function resolveDocPath(fromPath, relativePath) {
+  if (relativePath.startsWith("./") || relativePath.startsWith("../")) {
+    const fromDir = dirname3(fromPath);
+    const resolved = resolve2(fromDir, relativePath);
+    return relative3(".", resolved);
   }
-  return { projectId: project.id, projectRoot };
+  return relativePath;
 }
-function formatDocForDisplay(doc) {
+function checkStaleness(docPath, graph) {
+  const doc = graph.get(docPath);
+  if (!doc) {
+    return {
+      isStale: false,
+      staleDependencies: []
+    };
+  }
+  if (!doc.lastApprovedAt) {
+    return {
+      isStale: false,
+      staleDependencies: []
+    };
+  }
+  const staleDeps = [];
+  for (const depRelPath of doc.dependencies) {
+    const depAbsPath = resolveDocPath(docPath, depRelPath);
+    const depNode = graph.get(depAbsPath);
+    if (!depNode || !depNode.lastModifiedAt) {
+      continue;
+    }
+    if (depNode.lastModifiedAt > doc.lastApprovedAt) {
+      staleDeps.push({
+        path: depRelPath,
+        lastModified: depNode.lastModifiedAt,
+        parentApproved: doc.lastApprovedAt
+      });
+    }
+  }
+  const isStale = staleDeps.length > 0;
   return {
-    path: doc.path,
-    filename: doc.filename,
-    extension: doc.extension,
-    sync_status: doc.status,
-    has_frontmatter: doc.has_frontmatter ? "Yes" : "No",
-    meta_status: doc.meta_status ?? "-",
-    meta_version: doc.meta_version ?? "-",
-    meta_tldr: doc.meta_tldr ?? "-",
-    meta_modules: doc.meta_modules ? JSON.parse(doc.meta_modules).join(", ") : "-",
-    meta_dependencies: doc.meta_dependencies ? JSON.parse(doc.meta_dependencies).join(", ") : "-"
+    isStale,
+    reason: isStale ? `${staleDeps.length} dependencies modified since approval` : void 0,
+    staleDependencies: staleDeps
   };
 }
-docCommand.command("list").alias("ls").option("--meta-status <status>", "Filter by frontmatter status (DRAFT, IN-REVIEW, APPROVED, TEMPLATE)").option("--module <module>", "Filter by module").option("--with-frontmatter", "Only show documents with frontmatter").option("--without-frontmatter", "Only show documents without frontmatter (shadow mode)").option("--templates", "Only show TEMPLATE documents").option("--search <term>", "Search by tldr content").description("List documents with metadata filters").action((options) => {
-  const opts = getOutputOptions(docCommand);
-  const ctx = getProjectId(opts);
-  if (!ctx) {
+function checkCascadeApproval(docPath, graph) {
+  const doc = graph.get(docPath);
+  if (!doc) {
+    return {
+      canCascade: false,
+      affectedDocs: [],
+      blockedBy: []
+    };
+  }
+  const canApprove = [];
+  const blocked = [];
+  for (const dependentPath of doc.dependents) {
+    const dependent = graph.get(dependentPath);
+    if (!dependent) {
+      continue;
+    }
+    const allDepsApproved = dependent.dependencies.every((depRelPath) => {
+      const depAbsPath = resolveDocPath(dependentPath, depRelPath);
+      const depNode = graph.get(depAbsPath);
+      if (depAbsPath === docPath) {
+        return true;
+      }
+      return depNode && depNode.status === "APPROVED";
+    });
+    if (allDepsApproved) {
+      canApprove.push(dependentPath);
+    } else {
+      blocked.push(dependentPath);
+    }
+  }
+  return {
+    canCascade: canApprove.length > 0,
+    affectedDocs: canApprove,
+    blockedBy: blocked
+  };
+}
+function getTopologicalOrder(graph) {
+  const visited = /* @__PURE__ */ new Set();
+  const result = [];
+  function visit(path) {
+    if (visited.has(path)) {
+      return;
+    }
+    visited.add(path);
+    const node = graph.get(path);
+    if (!node) {
+      return;
+    }
+    for (const depRelPath of node.dependencies) {
+      const depAbsPath = resolveDocPath(path, depRelPath);
+      visit(depAbsPath);
+    }
+    result.push(path);
+  }
+  for (const path of graph.keys()) {
+    visit(path);
+  }
+  return result;
+}
+function getFoundationalDocs(graph) {
+  const foundational = [];
+  for (const [path, node] of graph.entries()) {
+    if (node.dependencies.length === 0) {
+      foundational.push(path);
+    }
+  }
+  return foundational;
+}
+function getDirectDependents(docPath, graph) {
+  const doc = graph.get(docPath);
+  return doc ? [...doc.dependents] : [];
+}
+function getTransitiveDependents(docPath, graph) {
+  const visited = /* @__PURE__ */ new Set();
+  const result = [];
+  function visit(path) {
+    if (visited.has(path)) {
+      return;
+    }
+    visited.add(path);
+    const node = graph.get(path);
+    if (!node) {
+      return;
+    }
+    for (const dependentPath of node.dependents) {
+      result.push(dependentPath);
+      visit(dependentPath);
+    }
+  }
+  visit(docPath);
+  return result;
+}
+
+// src/commands/doc.ts
+init_config();
+init_config();
+import { writeFileSync as writeFileSync5, readFileSync as readFileSync8 } from "fs";
+async function ensureProjectContext() {
+  const projectPath = findProjectRoot();
+  if (!projectPath) {
+    throw new Error('Not in an AIGILE project. Run "aigile init" first.');
+  }
+  const config = loadProjectConfig(projectPath);
+  if (!config) {
+    throw new Error("Could not load project config.");
+  }
+  const project = queryOne("SELECT id FROM projects WHERE key = ?", [
+    config.project.key
+  ]);
+  if (!project) {
+    throw new Error(`Project "${config.project.key}" not found in database.`);
+  }
+  return { projectId: project.id, projectPath, projectKey: config.project.key };
+}
+var integrityCommand = new Command19("integrity").description("Check document integrity and dependencies").option("--fix", "Auto-fix missing dependencies in frontmatter").option("--all", "Show all documents, not just problems").action(async (options) => {
+  const opts = getOutputOptions(integrityCommand);
+  const cwd = process.cwd();
+  try {
+    await runIntegrityCheck(cwd, options, opts);
+  } catch (err) {
+    error(err instanceof Error ? err.message : String(err), opts);
     process.exit(1);
   }
-  let documents = [];
-  if (options.metaStatus) {
-    documents = getDocumentsByMetaStatus(ctx.projectId, options.metaStatus);
-  } else if (options.module) {
-    documents = getDocumentsByModule(ctx.projectId, options.module);
-  } else if (options.withFrontmatter) {
-    documents = getDocumentsWithFrontmatter(ctx.projectId);
-  } else if (options.withoutFrontmatter) {
-    documents = getDocumentsWithoutFrontmatter(ctx.projectId);
-  } else if (options.templates) {
-    documents = getTemplateDocuments(ctx.projectId);
-  } else if (options.search) {
-    documents = searchDocumentsByTldr(ctx.projectId, options.search);
-  } else {
-    documents = getDocumentsWithFrontmatter(ctx.projectId);
+});
+var approveCommand = new Command19("approve").description("Approve a document").argument("<file>", "File path to approve").option("--cascade", "Auto-approve dependents if all their dependencies are approved").action(async (filePath, options) => {
+  const opts = getOutputOptions(approveCommand);
+  const cwd = process.cwd();
+  try {
+    await approveDocument(cwd, filePath, options, opts);
+  } catch (err) {
+    error(err instanceof Error ? err.message : String(err), opts);
+    process.exit(1);
   }
-  const displayDocs = documents.map(formatDocForDisplay);
-  data(
-    displayDocs,
-    [
-      { header: "Path", key: "path", width: 45 },
-      { header: "Status", key: "meta_status", width: 12 },
-      { header: "Version", key: "meta_version", width: 8 },
-      { header: "Modules", key: "meta_modules", width: 20 }
-    ],
-    opts
-  );
 });
-docCommand.command("show <path>").description("Show document details including frontmatter metadata").action((filePath) => {
-  const opts = getOutputOptions(docCommand);
-  const ctx = getProjectId(opts);
-  if (!ctx) {
+var ackCommand = new Command19("ack").description("Acknowledge document changes (clears STALE)").argument("<file>", "File path to acknowledge").action(async (filePath) => {
+  const opts = getOutputOptions(ackCommand);
+  const cwd = process.cwd();
+  try {
+    await acknowledgeDocument(cwd, filePath, opts);
+  } catch (err) {
+    error(err instanceof Error ? err.message : String(err), opts);
     process.exit(1);
   }
-  const doc = getDocumentByPath(ctx.projectId, filePath);
-  if (!doc) {
-    error(`Document not found: ${filePath}`, opts);
+});
+var readyCommand = new Command19("ready").description("Mark document as ready for review").argument("<file>", "File path to mark ready").action(async (filePath) => {
+  const opts = getOutputOptions(readyCommand);
+  const cwd = process.cwd();
+  try {
+    await markReady(cwd, filePath, opts);
+  } catch (err) {
+    error(err instanceof Error ? err.message : String(err), opts);
     process.exit(1);
   }
-  const fullPath = join8(ctx.projectRoot, filePath);
-  const parsed = parseFrontmatterFromFile(fullPath);
-  if (opts.json) {
-    console.log(JSON.stringify({
-      success: true,
-      data: {
-        database: doc,
-        frontmatter: parsed ? {
-          raw: parsed.raw,
-          metadata: parsed.metadata
-        } : null
-      }
-    }));
-  } else {
-    const displayData = {
-      path: doc.path,
-      filename: doc.filename,
-      extension: doc.extension,
-      sync_status: doc.status,
-      size_bytes: doc.size_bytes,
-      last_scanned: doc.last_scanned_at,
-      has_frontmatter: doc.has_frontmatter ? "Yes" : "No"
-    };
-    if (parsed) {
-      displayData.meta_status = parsed.metadata.status ?? "-";
-      displayData.meta_version = parsed.metadata.version ?? "-";
-      displayData.meta_tldr = parsed.metadata.tldr ?? "-";
-      displayData.meta_title = parsed.metadata.title ?? "-";
-      displayData.meta_modules = parsed.metadata.modules?.join(", ") ?? "-";
-      displayData.meta_dependencies = parsed.metadata.dependencies?.join(", ") ?? "-";
-      displayData.meta_code_refs = parsed.metadata.code_refs?.join(", ") ?? "-";
-      displayData.meta_authors = parsed.metadata.authors?.join(", ") ?? "-";
-    }
-    details(
-      displayData,
-      [
-        { label: "Path", key: "path" },
-        { label: "Filename", key: "filename" },
-        { label: "Extension", key: "extension" },
-        { label: "Sync Status", key: "sync_status" },
-        { label: "Size (bytes)", key: "size_bytes" },
-        { label: "Last Scanned", key: "last_scanned" },
-        { label: "Has Frontmatter", key: "has_frontmatter" },
-        { label: "Meta Status", key: "meta_status" },
-        { label: "Meta Version", key: "meta_version" },
-        { label: "Meta Title", key: "meta_title" },
-        { label: "Meta TLDR", key: "meta_tldr" },
-        { label: "Meta Modules", key: "meta_modules" },
-        { label: "Meta Dependencies", key: "meta_dependencies" },
-        { label: "Meta Code Refs", key: "meta_code_refs" },
-        { label: "Meta Authors", key: "meta_authors" }
-      ],
-      opts
-    );
+});
+var reviewCommand = new Command19("review").description("Interactive document review (TUI)").action(async () => {
+  const opts = getOutputOptions(reviewCommand);
+  warning("Interactive review TUI not yet implemented", opts);
+  info("Use 'aigile doc integrity' to see document status", opts);
+});
+var exceptionCommand = new Command19("exception").description("Mark document with structural exception").argument("<file>", "File path").argument("<reason>", "Reason for exception").action(async (filePath, reason) => {
+  const opts = getOutputOptions(exceptionCommand);
+  const cwd = process.cwd();
+  try {
+    await markException(cwd, filePath, reason, opts);
+  } catch (err) {
+    error(err instanceof Error ? err.message : String(err), opts);
+    process.exit(1);
   }
 });
-docCommand.command("update <path>").option("--status <status>", "Set metadata status (DRAFT, IN-REVIEW, APPROVED, TEMPLATE, PRODUCTION)").option("--version <version>", "Set metadata version").option("--tldr <tldr>", "Set one-sentence summary").option("--title <title>", "Set document title").option("--add-module <module>", "Add a module to the modules list").option("--add-dependency <dep>", "Add a dependency path").option("--add-code-ref <ref>", "Add a code reference path").option("--add-author <author>", "Add an author").option("--dry-run", "Show what would be changed without modifying file").description("Update frontmatter metadata in a document").action((filePath, options) => {
-  const opts = getOutputOptions(docCommand);
-  const ctx = getProjectId(opts);
-  if (!ctx) {
+var refactorCommand = new Command19("refactor").description("Mark document for refactoring").argument("<file>", "File path").action(async (filePath) => {
+  const opts = getOutputOptions(refactorCommand);
+  const cwd = process.cwd();
+  try {
+    await markRefactoring(cwd, filePath, opts);
+  } catch (err) {
+    error(err instanceof Error ? err.message : String(err), opts);
     process.exit(1);
   }
-  const fullPath = join8(ctx.projectRoot, filePath);
-  let content;
+});
+var archiveCommand = new Command19("archive").description("Archive a document").argument("<file>", "File path to archive").action(async (filePath) => {
+  const opts = getOutputOptions(archiveCommand);
+  const cwd = process.cwd();
   try {
-    content = readFileSync7(fullPath, "utf-8");
-  } catch {
-    error(`Could not read file: ${filePath}`, opts);
+    await archiveDocument(cwd, filePath, opts);
+  } catch (err) {
+    error(err instanceof Error ? err.message : String(err), opts);
     process.exit(1);
   }
-  const updates = {};
-  if (options.status) {
-    updates.status = options.status;
+});
+async function runIntegrityCheck(cwd, options, opts) {
+  const config = loadProjectConfig(cwd);
+  if (!config?.project?.key) {
+    throw new Error("AIGILE not initialized in this directory");
+  }
+  const projectId = config.project.key;
+  const graph = buildDependencyGraph(projectId);
+  blank();
+  header("Document Integrity Check", opts);
+  blank();
+  const orderedDocs = getTopologicalOrder(graph);
+  let issueCount = 0;
+  const stale = [];
+  const needsReview = [];
+  const templates = [];
+  for (const docPath of orderedDocs) {
+    const node = graph.get(docPath);
+    if (!node) continue;
+    const stalenessCheck = checkStaleness(docPath, graph);
+    const hasIssues = stalenessCheck.isStale || node.status === "NEEDS_REVIEW" || node.status === "TEMPLATE";
+    if (!hasIssues && !options.all) {
+      continue;
+    }
+    console.log(`\u{1F4C4} ${docPath}`);
+    console.log(`   Status: ${node.status}`);
+    if (stalenessCheck.isStale) {
+      console.log(`   \u26A0\uFE0F  STALE: ${stalenessCheck.reason}`);
+      stale.push(docPath);
+      issueCount++;
+    }
+    if (node.status === "NEEDS_REVIEW") {
+      console.log(`   \u{1F4DD} Needs review`);
+      needsReview.push(docPath);
+      issueCount++;
+    }
+    if (node.status === "TEMPLATE") {
+      console.log(`   \u{1F4CB} Template (needs filling)`);
+      templates.push(docPath);
+      issueCount++;
+    }
+    if (node.dependencies.length > 0) {
+      console.log(`   Dependencies: ${node.dependencies.join(", ")}`);
+    }
+    if (node.dependents.length > 0) {
+      console.log(`   Dependents: ${node.dependents.length} files`);
+    }
+    blank();
+  }
+  blank();
+  header("Summary", opts);
+  console.log(`  Total documents: ${orderedDocs.length}`);
+  console.log(`  Issues found: ${issueCount}`);
+  if (stale.length > 0) {
+    console.log(`    - Stale: ${stale.length}`);
+  }
+  if (needsReview.length > 0) {
+    console.log(`    - Needs review: ${needsReview.length}`);
+  }
+  if (templates.length > 0) {
+    console.log(`    - Templates: ${templates.length}`);
+  }
+  blank();
+  if (issueCount === 0) {
+    success("\u2713 All documents are up to date", opts);
+  } else {
+    info("Run 'aigile doc approve <file>' to approve documents", opts);
+    info("Run 'aigile doc ack <file>' to acknowledge changes", opts);
+  }
+}
+async function approveDocument(cwd, filePath, options, opts) {
+  const config = loadProjectConfig(cwd);
+  if (!config?.project?.key) {
+    throw new Error("AIGILE not initialized in this directory");
+  }
+  const absolutePath = resolve3(cwd, filePath);
+  if (!existsSync7(absolutePath)) {
+    throw new Error(`File not found: ${filePath}`);
+  }
+  const projectId = config.project.key;
+  const relativePath = relative4(cwd, absolutePath);
+  const doc = queryOne(
+    `SELECT id, meta_status FROM documents WHERE project_id = ? AND path = ?`,
+    [projectId, relativePath]
+  );
+  if (!doc) {
+    throw new Error(`Document not found in database: ${filePath}`);
+  }
+  const content = readFileSync8(absolutePath, "utf-8");
+  const now = (/* @__PURE__ */ new Date()).toISOString().split("T")[0];
+  const updatedContent = updateFrontmatterContent(content, {
+    status: "APPROVED",
+    reviewed: now
+  });
+  writeFileSync5(absolutePath, updatedContent, "utf-8");
+  run(`UPDATE documents SET meta_status = ?, last_approved_at = ?, reviewed_at = ? WHERE id = ?`, [
+    "APPROVED",
+    now,
+    now,
+    doc.id
+  ]);
+  success(`\u2713 Approved: ${filePath}`, opts);
+  if (options.cascade) {
+    const graph = buildDependencyGraph(projectId);
+    const cascadeResult = checkCascadeApproval(relativePath, graph);
+    if (cascadeResult.canCascade && cascadeResult.affectedDocs.length > 0) {
+      blank();
+      info(`Cascade approving ${cascadeResult.affectedDocs.length} dependents...`, opts);
+      for (const depPath of cascadeResult.affectedDocs) {
+        const depAbsolute = resolve3(cwd, depPath);
+        const depContent = readFileSync8(depAbsolute, "utf-8");
+        const updatedDep = updateFrontmatterContent(depContent, {
+          status: "APPROVED",
+          reviewed: now
+        });
+        writeFileSync5(depAbsolute, updatedDep, "utf-8");
+        const depDoc = queryOne(
+          `SELECT id FROM documents WHERE project_id = ? AND path = ?`,
+          [projectId, depPath]
+        );
+        if (depDoc) {
+          run(
+            `UPDATE documents SET meta_status = ?, last_approved_at = ?, reviewed_at = ? WHERE id = ?`,
+            ["APPROVED", now, now, depDoc.id]
+          );
+        }
+        success(`  \u2713 ${depPath}`, opts);
+      }
+    }
+  }
+}
+async function acknowledgeDocument(cwd, filePath, opts) {
+  const config = loadProjectConfig(cwd);
+  if (!config?.project?.key) {
+    throw new Error("AIGILE not initialized in this directory");
+  }
+  const absolutePath = resolve3(cwd, filePath);
+  if (!existsSync7(absolutePath)) {
+    throw new Error(`File not found: ${filePath}`);
+  }
+  const projectId = config.project.key;
+  const relativePath = relative4(cwd, absolutePath);
+  const doc = queryOne(
+    `SELECT id FROM documents WHERE project_id = ? AND path = ?`,
+    [projectId, relativePath]
+  );
+  if (!doc) {
+    throw new Error(`Document not found in database: ${filePath}`);
+  }
+  const now = (/* @__PURE__ */ new Date()).toISOString().split("T")[0];
+  run(`UPDATE documents SET last_approved_at = ? WHERE id = ?`, [now, doc.id]);
+  success(`\u2713 Acknowledged: ${filePath}`, opts);
+  info("Document is no longer marked as stale", opts);
+}
+async function markReady(cwd, filePath, opts) {
+  const config = loadProjectConfig(cwd);
+  if (!config?.project?.key) {
+    throw new Error("AIGILE not initialized in this directory");
+  }
+  const absolutePath = resolve3(cwd, filePath);
+  if (!existsSync7(absolutePath)) {
+    throw new Error(`File not found: ${filePath}`);
+  }
+  const projectId = config.project.key;
+  const relativePath = relative4(cwd, absolutePath);
+  const content = readFileSync8(absolutePath, "utf-8");
+  const updatedContent = updateFrontmatterContent(content, {
+    status: "NEEDS_REVIEW"
+  });
+  writeFileSync5(absolutePath, updatedContent, "utf-8");
+  const doc = queryOne(
+    `SELECT id FROM documents WHERE project_id = ? AND path = ?`,
+    [projectId, relativePath]
+  );
+  if (doc) {
+    run(`UPDATE documents SET meta_status = ?, needs_review = 1 WHERE id = ?`, [
+      "NEEDS_REVIEW",
+      doc.id
+    ]);
+  }
+  success(`\u2713 Marked ready for review: ${filePath}`, opts);
+}
+async function markException(cwd, filePath, reason, opts) {
+  const config = loadProjectConfig(cwd);
+  if (!config?.project?.key) {
+    throw new Error("AIGILE not initialized in this directory");
   }
-  if (options.version) {
-    updates.version = options.version;
+  const absolutePath = resolve3(cwd, filePath);
+  if (!existsSync7(absolutePath)) {
+    throw new Error(`File not found: ${filePath}`);
   }
-  if (options.tldr) {
-    updates.tldr = options.tldr;
+  const projectId = config.project.key;
+  const relativePath = relative4(cwd, absolutePath);
+  const content = readFileSync8(absolutePath, "utf-8");
+  const updatedContent = updateFrontmatterContent(content, {
+    exception: reason
+  });
+  writeFileSync5(absolutePath, updatedContent, "utf-8");
+  const doc = queryOne(
+    `SELECT id FROM documents WHERE project_id = ? AND path = ?`,
+    [projectId, relativePath]
+  );
+  if (doc) {
+    run(`UPDATE documents SET meta_exception = ? WHERE id = ?`, [reason, doc.id]);
+  }
+  success(`\u2713 Marked exception: ${filePath}`, opts);
+  info(`Reason: ${reason}`, opts);
+}
+async function markRefactoring(cwd, filePath, opts) {
+  const config = loadProjectConfig(cwd);
+  if (!config?.project?.key) {
+    throw new Error("AIGILE not initialized in this directory");
+  }
+  const absolutePath = resolve3(cwd, filePath);
+  if (!existsSync7(absolutePath)) {
+    throw new Error(`File not found: ${filePath}`);
   }
-  if (options.title) {
-    updates.title = options.title;
+  const projectId = config.project.key;
+  const relativePath = relative4(cwd, absolutePath);
+  const doc = queryOne(
+    `SELECT id FROM documents WHERE project_id = ? AND path = ?`,
+    [projectId, relativePath]
+  );
+  if (!doc) {
+    throw new Error(`Document not found in database: ${filePath}`);
+  }
+  run(`UPDATE documents SET monitoring_category = ? WHERE id = ?`, [
+    "REFACTORING_REQUIRED",
+    doc.id
+  ]);
+  success(`\u2713 Marked for refactoring: ${filePath}`, opts);
+  info("This file needs to be moved or restructured", opts);
+}
+async function archiveDocument(cwd, filePath, opts) {
+  const config = loadProjectConfig(cwd);
+  if (!config?.project?.key) {
+    throw new Error("AIGILE not initialized in this directory");
+  }
+  const absolutePath = resolve3(cwd, filePath);
+  if (!existsSync7(absolutePath)) {
+    throw new Error(`File not found: ${filePath}`);
+  }
+  const projectId = config.project.key;
+  const relativePath = relative4(cwd, absolutePath);
+  const content = readFileSync8(absolutePath, "utf-8");
+  const updatedContent = updateFrontmatterContent(content, {
+    status: "ARCHIVED"
+  });
+  writeFileSync5(absolutePath, updatedContent, "utf-8");
+  const doc = queryOne(
+    `SELECT id FROM documents WHERE project_id = ? AND path = ?`,
+    [projectId, relativePath]
+  );
+  if (doc) {
+    run(`UPDATE documents SET meta_status = ? WHERE id = ?`, ["ARCHIVED", doc.id]);
   }
-  if (options.addModule) {
-    updates.modules = [options.addModule];
+  success(`\u2713 Archived: ${filePath}`, opts);
+  info("Document moved to archived status", opts);
+}
+var dependentsCommand = new Command19("dependents").description("Show documents that depend on the specified file").argument("<file>", "Document path (relative to project root)").option("--depth <n>", "Maximum depth to traverse (default: unlimited)", parseInt).option("--json", "Output as JSON").action(async (file, opts) => {
+  const { projectId, projectPath } = await ensureProjectContext();
+  const filePath = file.startsWith(".aigile/") ? file : `.aigile/${file}`;
+  const graph = buildDependencyGraph(projectId);
+  const doc = graph.get(filePath);
+  if (!doc) {
+    error(`Document not found: ${filePath}`);
+    process.exit(1);
   }
-  if (options.addDependency) {
-    updates.dependencies = [options.addDependency];
+  const directDependents = getDirectDependents(filePath, graph);
+  const allDependents = opts.depth === 1 ? directDependents : getTransitiveDependents(filePath, graph);
+  if (opts.json) {
+    console.log(
+      JSON.stringify(
+        {
+          document: filePath,
+          directDependents,
+          allDependents,
+          count: allDependents.length
+        },
+        null,
+        2
+      )
+    );
+    return;
   }
-  if (options.addCodeRef) {
-    updates.code_refs = [options.addCodeRef];
+  success(`Dependents of: ${filePath}`, opts);
+  console.log();
+  if (allDependents.length === 0) {
+    info("No dependents found (this is a leaf document)", opts);
+    return;
   }
-  if (options.addAuthor) {
-    updates.authors = [options.addAuthor];
+  console.log(`Total: ${allDependents.length} dependent(s)`);
+  console.log();
+  for (const depPath of allDependents) {
+    const depDoc = graph.get(depPath);
+    const tldr = depDoc?.status ? `[${depDoc.status}]` : "";
+    console.log(`  \u2022 ${depPath} ${tldr}`);
   }
-  if (Object.keys(updates).length === 0) {
-    error("No updates specified. Use --status, --version, --tldr, etc.", opts);
+});
+var dependenciesCommand = new Command19("dependencies").description("Show documents that the specified file depends on").argument("<file>", "Document path (relative to project root)").option("--json", "Output as JSON").action(async (file, opts) => {
+  const { projectId, projectPath } = await ensureProjectContext();
+  const filePath = file.startsWith(".aigile/") ? file : `.aigile/${file}`;
+  const graph = buildDependencyGraph(projectId);
+  const doc = graph.get(filePath);
+  if (!doc) {
+    error(`Document not found: ${filePath}`);
     process.exit(1);
   }
-  const newContent = updateFrontmatterContent(content, updates);
-  if (options.dryRun) {
+  const dependencies = doc.dependencies || [];
+  if (opts.json) {
+    console.log(
+      JSON.stringify(
+        {
+          document: filePath,
+          dependencies,
+          count: dependencies.length
+        },
+        null,
+        2
+      )
+    );
+    return;
+  }
+  success(`Dependencies of: ${filePath}`, opts);
+  console.log();
+  if (dependencies.length === 0) {
+    info("No dependencies (this is a foundational document)", opts);
+    return;
+  }
+  console.log(
+    `Total: ${dependencies.length} dependenc${dependencies.length === 1 ? "y" : "ies"}`
+  );
+  console.log();
+  for (const depPath of dependencies) {
+    const depDoc = graph.get(depPath);
+    const tldr = depDoc?.status ? `[${depDoc.status}]` : "";
+    console.log(`  \u2022 ${depPath} ${tldr}`);
+  }
+});
+var nextTemplateCommand = new Command19("next-template").description("Find the next template document to fill (foundation-first)").option("--json", "Output as JSON").action(async (opts) => {
+  const { projectId } = await ensureProjectContext();
+  const templates = queryAll(
+    `SELECT path, meta_tldr, meta_dependencies
+       FROM documents
+       WHERE project_id = ? AND meta_status = 'TEMPLATE'
+       ORDER BY path ASC`,
+    [projectId]
+  );
+  if (templates.length === 0) {
     if (opts.json) {
-      console.log(JSON.stringify({
-        success: true,
-        dryRun: true,
-        updates,
-        preview: newContent.substring(0, 500) + (newContent.length > 500 ? "..." : "")
-      }));
-    } else {
-      info("Dry run - would update frontmatter with:", opts);
-      console.log(JSON.stringify(updates, null, 2));
-      console.log("\nNew frontmatter preview:");
-      const lines = newContent.split("\n");
-      const endIndex = lines.findIndex((l, i) => i > 0 && l === "---");
-      lines.slice(0, endIndex + 1).forEach((l) => console.log(l));
+      console.log(JSON.stringify({ nextTemplate: null, remaining: 0 }, null, 2));
+      return;
     }
+    success("\u2713 No templates remaining - all documents filled!", opts);
     return;
   }
-  try {
-    writeFileSync5(fullPath, newContent, "utf-8");
-    success(`Updated frontmatter in ${filePath}`, opts);
-    if (!opts.json) {
-      info('Run "aigile sync scan" to update the database.', opts);
-    }
-  } catch (err) {
-    error(`Could not write file: ${filePath}`, opts);
-    process.exit(1);
-  }
-});
-docCommand.command("init-frontmatter <path>").option("--status <status>", "Initial status (default: DRAFT)").option("--version <version>", "Initial version (default: 0.1)").option("--tldr <tldr>", "One-sentence summary").option("--title <title>", "Document title").description("Add frontmatter to a file that does not have it").action((filePath, options) => {
-  const opts = getOutputOptions(docCommand);
-  const ctx = getProjectId(opts);
-  if (!ctx) {
-    process.exit(1);
+  const graph = buildDependencyGraph(projectId);
+  const foundational = getFoundationalDocs(graph).filter((path) => {
+    const doc = graph.get(path);
+    return doc?.status === "TEMPLATE";
+  });
+  const nextTemplate = foundational[0] || templates[0].path;
+  const nextDoc = graph.get(nextTemplate);
+  if (opts.json) {
+    console.log(
+      JSON.stringify(
+        {
+          nextTemplate,
+          tldr: nextDoc?.status || null,
+          remaining: templates.length,
+          foundational: foundational.length
+        },
+        null,
+        2
+      )
+    );
+    return;
   }
-  const fullPath = join8(ctx.projectRoot, filePath);
-  let content;
-  try {
-    content = readFileSync7(fullPath, "utf-8");
-  } catch {
-    error(`Could not read file: ${filePath}`, opts);
-    process.exit(1);
+  success(`Next template to fill: ${nextTemplate}`, opts);
+  if (nextDoc?.status) {
+    info(`TLDR: ${nextDoc.status}`, opts);
   }
-  const existing = parseFrontmatterFromFile(fullPath);
-  if (existing) {
-    error('File already has frontmatter. Use "aigile doc update" instead.', opts);
-    process.exit(1);
+  console.log();
+  info(`Remaining templates: ${templates.length}`, opts);
+  info(`Foundational templates: ${foundational.length}`, opts);
+});
+var statsCommand = new Command19("stats").description("Show document statistics and progress").option("--json", "Output as JSON").action(async (opts) => {
+  const { projectId } = await ensureProjectContext();
+  const statusCounts = queryAll(
+    `SELECT meta_status, COUNT(*) as count
+       FROM documents
+       WHERE project_id = ? AND meta_status IS NOT NULL
+       GROUP BY meta_status`,
+    [projectId]
+  );
+  const stats = {};
+  let total = 0;
+  for (const row of statusCounts) {
+    stats[row.meta_status || "UNKNOWN"] = row.count;
+    total += row.count;
   }
-  const metadata = {
-    status: options.status ?? "DRAFT",
-    version: options.version ?? "0.1",
-    tldr: options.tldr ?? "",
-    title: options.title
-  };
-  const newContent = updateFrontmatterContent(content, metadata);
-  try {
-    writeFileSync5(fullPath, newContent, "utf-8");
-    success(`Added frontmatter to ${filePath}`, opts);
-    if (!opts.json) {
-      info('Run "aigile sync scan" to update the database.', opts);
+  const graph = buildDependencyGraph(projectId);
+  let staleCount = 0;
+  for (const [path] of graph) {
+    const staleness = checkStaleness(path, graph);
+    if (staleness.isStale) {
+      staleCount++;
     }
-  } catch {
-    error(`Could not write file: ${filePath}`, opts);
-    process.exit(1);
-  }
-});
-docCommand.command("stats").description("Show frontmatter statistics for the project").action(() => {
-  const opts = getOutputOptions(docCommand);
-  const ctx = getProjectId(opts);
-  if (!ctx) {
-    process.exit(1);
   }
-  const withFrontmatter = getDocumentsWithFrontmatter(ctx.projectId);
-  const withoutFrontmatter = getDocumentsWithoutFrontmatter(ctx.projectId);
-  const templates = getTemplateDocuments(ctx.projectId);
-  const drafts = getDocumentsByMetaStatus(ctx.projectId, "DRAFT");
-  const inReview = getDocumentsByMetaStatus(ctx.projectId, "IN-REVIEW");
-  const approved = getDocumentsByMetaStatus(ctx.projectId, "APPROVED");
-  const stats = {
-    total_documents: withFrontmatter.length + withoutFrontmatter.length,
-    with_frontmatter: withFrontmatter.length,
-    without_frontmatter: withoutFrontmatter.length,
-    templates: templates.length,
-    drafts: drafts.length,
-    in_review: inReview.length,
-    approved: approved.length
-  };
   if (opts.json) {
-    console.log(JSON.stringify({ success: true, data: stats }));
-  } else {
-    details(
-      stats,
-      [
-        { label: "Total Documents", key: "total_documents" },
-        { label: "With Frontmatter", key: "with_frontmatter" },
-        { label: "Without Frontmatter", key: "without_frontmatter" },
-        { label: "TEMPLATE", key: "templates" },
-        { label: "DRAFT", key: "drafts" },
-        { label: "IN-REVIEW", key: "in_review" },
-        { label: "APPROVED", key: "approved" }
-      ],
-      opts
+    console.log(
+      JSON.stringify(
+        {
+          total,
+          byStatus: stats,
+          stale: staleCount,
+          completion: total > 0 ? Math.round((stats.APPROVED || 0) / total * 100) : 0
+        },
+        null,
+        2
+      )
     );
+    return;
+  }
+  success("Document Statistics", opts);
+  console.log();
+  console.log(`Total Documents: ${total}`);
+  console.log();
+  if (Object.keys(stats).length > 0) {
+    console.log("By Status:");
+    for (const [status, count] of Object.entries(stats)) {
+      const pct = total > 0 ? (count / total * 100).toFixed(1) : "0.0";
+      console.log(`  ${status.padEnd(15)} ${count.toString().padStart(4)} (${pct}%)`);
+    }
+    console.log();
+  }
+  if (staleCount > 0) {
+    warning(`\u26A0 ${staleCount} document(s) are stale (dependencies changed)`, opts);
   }
+  const approved = stats.APPROVED || 0;
+  const completion = total > 0 ? (approved / total * 100).toFixed(1) : "0.0";
+  info(`Completion: ${completion}% (${approved}/${total} approved)`, opts);
 });
+var docCommand = new Command19("doc").description("Document integrity and status management commands").addCommand(integrityCommand).addCommand(approveCommand).addCommand(ackCommand).addCommand(readyCommand).addCommand(reviewCommand).addCommand(exceptionCommand).addCommand(refactorCommand).addCommand(archiveCommand).addCommand(dependentsCommand).addCommand(dependenciesCommand).addCommand(nextTemplateCommand).addCommand(statsCommand);
 
 // src/commands/daemon.ts
 init_connection();
 import { Command as Command20 } from "commander";
-import { existsSync as existsSync9, writeFileSync as writeFileSync6, unlinkSync, readFileSync as readFileSync9, mkdirSync as mkdirSync5, statSync as statSync3, renameSync, readdirSync as readdirSync2 } from "fs";
-import { join as join11, dirname as dirname3 } from "path";
+import { existsSync as existsSync11, writeFileSync as writeFileSync7, unlinkSync, readFileSync as readFileSync11, mkdirSync as mkdirSync5, statSync as statSync5, renameSync, readdirSync as readdirSync3 } from "fs";
+import { join as join12, dirname as dirname4 } from "path";
 import { homedir as homedir2, platform } from "os";
 import { spawn, execSync as execSync2 } from "child_process";
 init_config();
 
 // src/services/daemon-manager.ts
-import { existsSync as existsSync8 } from "fs";
-import { join as join10 } from "path";
+import { existsSync as existsSync10 } from "fs";
+import { join as join11 } from "path";
 import { EventEmitter as EventEmitter2 } from "events";
 
 // src/services/file-watcher.ts
 init_connection();
 import { watch } from "chokidar";
-import { relative as relative3, extname as extname2, basename as basename4 } from "path";
-import { readFileSync as readFileSync8, statSync as statSync2 } from "fs";
+import { relative as relative5, extname as extname2, basename as basename4 } from "path";
+import { existsSync as existsSync9, readFileSync as readFileSync10, statSync as statSync4 } from "fs";
 import { EventEmitter } from "events";
 init_monitoring_patterns();
 init_config();
+
+// src/services/document-status-transitions.ts
+init_connection();
+import { writeFileSync as writeFileSync6, readFileSync as readFileSync9, existsSync as existsSync8 } from "fs";
+import { resolve as resolve4 } from "path";
+import { createHash as createHash2 } from "crypto";
+async function handleDocumentEdit(projectId, docPath, absolutePath) {
+  if (!existsSync8(absolutePath)) {
+    return false;
+  }
+  const doc = queryOne(
+    `SELECT id, meta_status, content_hash FROM documents WHERE project_id = ? AND path = ?`,
+    [projectId, docPath]
+  );
+  if (!doc) {
+    return false;
+  }
+  const currentStatus = doc.meta_status;
+  if (!currentStatus || currentStatus === "ARCHIVED") {
+    return false;
+  }
+  try {
+    const parsed = parseFrontmatterFromFile(absolutePath);
+    const fileStatus = parsed?.metadata?.status;
+    const content = readFileSync9(absolutePath, "utf-8");
+    const contentHash = createHash2("sha256").update(content).digest("hex");
+    if (contentHash === doc.content_hash) {
+      return false;
+    }
+    let newStatus = null;
+    switch (currentStatus) {
+      case "TEMPLATE":
+        newStatus = "DRAFT";
+        break;
+      case "APPROVED":
+        newStatus = "NEEDS_REVIEW";
+        break;
+      case "NEEDS_REVIEW":
+      case "DRAFT":
+        break;
+    }
+    if (!newStatus) {
+      return false;
+    }
+    const updatedContent = updateFrontmatterContent(content, {
+      status: newStatus
+    });
+    writeFileSync6(absolutePath, updatedContent, "utf-8");
+    const now = (/* @__PURE__ */ new Date()).toISOString().split("T")[0];
+    run(
+      `UPDATE documents 
+       SET meta_status = ?, content_hash = ?, last_modified_at = ?, needs_review = ?
+       WHERE id = ?`,
+      [
+        newStatus,
+        contentHash,
+        now,
+        newStatus === "NEEDS_REVIEW" ? 1 : 0,
+        doc.id
+      ]
+    );
+    console.log(
+      `[${(/* @__PURE__ */ new Date()).toISOString()}] Status transition: ${docPath} (${currentStatus} \u2192 ${newStatus})`
+    );
+    return true;
+  } catch (err) {
+    console.error(
+      `[${(/* @__PURE__ */ new Date()).toISOString()}] Error in status transition for ${docPath}: ${err}`
+    );
+    return false;
+  }
+}
+async function markDependentsStale(projectId, docPath) {
+  const dependents = queryAll(
+    `SELECT id, path, meta_dependencies FROM documents WHERE project_id = ?`,
+    [projectId]
+  );
+  let markedCount = 0;
+  for (const dep of dependents) {
+    try {
+      const dependencies = dep.meta_dependencies ? JSON.parse(dep.meta_dependencies) : [];
+      if (dependencies.includes(docPath)) {
+        run(`UPDATE documents SET needs_review = 1 WHERE id = ?`, [dep.id]);
+        markedCount++;
+      }
+    } catch {
+    }
+  }
+  if (markedCount > 0) {
+    console.log(
+      `[${(/* @__PURE__ */ new Date()).toISOString()}] Marked ${markedCount} dependents as stale for ${docPath}`
+    );
+  }
+  return markedCount;
+}
+function isAigileDoc(docPath) {
+  return docPath.startsWith(".aigile/") && (docPath.endsWith(".md") || docPath.endsWith(".feature"));
+}
+async function onFileChanged(projectId, projectPath, relativeDocPath) {
+  if (!isAigileDoc(relativeDocPath)) {
+    return;
+  }
+  const absolutePath = resolve4(projectPath, relativeDocPath);
+  const transitioned = await handleDocumentEdit(
+    projectId,
+    relativeDocPath,
+    absolutePath
+  );
+  if (transitioned || existsSync8(absolutePath)) {
+    await markDependentsStale(projectId, relativeDocPath);
+  }
+}
+
+// src/services/file-watcher.ts
 import picomatch2 from "picomatch";
 var FileWatcher = class extends EventEmitter {
   watcher = null;
   config;
   stats;
   debounceTimers = /* @__PURE__ */ new Map();
+  cleanupInterval = null;
   // Tri-state pattern matchers
   allowMatcher = null;
   denyMatcher = null;
@@ -8817,6 +8735,12 @@ var FileWatcher = class extends EventEmitter {
       this.updateCategoryCounts();
       this.emit("ready", this.stats);
     });
+    this.cleanupInterval = setInterval(
+      () => {
+        this.cleanupStaleTimers();
+      },
+      5 * 60 * 1e3
+    );
   }
   /**
    * Update category counts from database
@@ -8824,12 +8748,15 @@ var FileWatcher = class extends EventEmitter {
    */
   updateCategoryCounts() {
     try {
-      const counts = queryAll(`
+      const counts = queryAll(
+        `
         SELECT monitoring_category, COUNT(*) as count
         FROM documents
         WHERE project_id = ? AND status != 'deleted'
         GROUP BY monitoring_category
-      `, [this.config.projectId]);
+      `,
+        [this.config.projectId]
+      );
       this.stats.categoryCounts = { allow: 0, deny: 0, unknown: 0 };
       for (const row of counts) {
         const cat = row.monitoring_category;
@@ -8847,6 +8774,10 @@ var FileWatcher = class extends EventEmitter {
     if (!this.watcher) {
       return;
     }
+    if (this.cleanupInterval) {
+      clearInterval(this.cleanupInterval);
+      this.cleanupInterval = null;
+    }
     for (const timer of this.debounceTimers.values()) {
       clearTimeout(timer);
     }
@@ -8856,6 +8787,28 @@ var FileWatcher = class extends EventEmitter {
     this.stats.isRunning = false;
     this.emit("stopped");
   }
+  /**
+   * Periodic cleanup of stale debounce timers
+   * Removes timers for files that no longer exist
+   */
+  cleanupStaleTimers() {
+    const staleKeys = [];
+    for (const [path] of this.debounceTimers) {
+      if (!existsSync9(path)) {
+        staleKeys.push(path);
+      }
+    }
+    for (const key of staleKeys) {
+      const timer = this.debounceTimers.get(key);
+      if (timer) {
+        clearTimeout(timer);
+        this.debounceTimers.delete(key);
+      }
+    }
+    if (staleKeys.length > 0) {
+      console.log(`[FileWatcher] Cleaned up ${staleKeys.length} stale debounce timers`);
+    }
+  }
   /**
    * Get current watcher statistics
    */
@@ -8881,6 +8834,11 @@ var FileWatcher = class extends EventEmitter {
     const existingTimer = this.debounceTimers.get(absolutePath);
     if (existingTimer) {
       clearTimeout(existingTimer);
+      this.debounceTimers.delete(absolutePath);
+    }
+    if (type === "unlink") {
+      this.processFileEvent(type, absolutePath);
+      return;
     }
     const timer = setTimeout(() => {
       this.debounceTimers.delete(absolutePath);
@@ -8892,7 +8850,7 @@ var FileWatcher = class extends EventEmitter {
    * Process a file event (after debounce)
    */
   processFileEvent(type, absolutePath) {
-    const relativePath = relative3(this.config.projectPath, absolutePath);
+    const relativePath = relative5(this.config.projectPath, absolutePath);
     const category = this.classifyFile(relativePath);
     if (category === "deny" && type !== "unlink") {
       return;
@@ -8915,6 +8873,14 @@ var FileWatcher = class extends EventEmitter {
           break;
         case "change":
           this.syncFileChange(absolutePath, relativePath, category);
+          onFileChanged(this.config.projectId, this.config.projectPath, relativePath).catch((err) => {
+            this.emit("transitionError", {
+              path: relativePath,
+              error: err,
+              timestamp: /* @__PURE__ */ new Date()
+            });
+            console.error(`[FileWatcher] Error in onFileChanged for ${relativePath}:`, err);
+          });
           break;
         case "unlink":
           this.syncFileDelete(relativePath);
@@ -8933,7 +8899,7 @@ var FileWatcher = class extends EventEmitter {
     const filename = basename4(relativePath);
     const isBinary = isBinaryExtension(ext);
     try {
-      const stats = statSync2(absolutePath);
+      const stats = statSync4(absolutePath);
       const shouldComputeHash = category === "allow" || !isBinary && stats.size < 10 * 1024 * 1024;
       const hash = shouldComputeHash ? computeFileHash(absolutePath) : null;
       let hasFrontmatter = false;
@@ -8952,16 +8918,36 @@ var FileWatcher = class extends EventEmitter {
         [this.config.projectId, relativePath]
       );
       if (existing) {
-        this.updateDocument(existing.id, hash, stats.size, hasFrontmatter, frontmatterRaw, metadata, category);
+        this.updateDocument(
+          existing.id,
+          hash,
+          stats.size,
+          hasFrontmatter,
+          frontmatterRaw,
+          metadata,
+          category
+        );
       } else {
-        this.insertDocument(relativePath, filename, ext, hash, stats.size, hasFrontmatter, frontmatterRaw, metadata, category);
+        this.insertDocument(
+          relativePath,
+          filename,
+          ext,
+          hash,
+          stats.size,
+          hasFrontmatter,
+          frontmatterRaw,
+          metadata,
+          category
+        );
       }
     } catch (err) {
       const errMsg = err instanceof Error ? err.message : String(err);
       if (errMsg.includes("Database") || errMsg.includes("database")) {
         throw err;
       }
-      console.error(`[${(/* @__PURE__ */ new Date()).toISOString()}] syncFileAdd error for ${relativePath}: ${errMsg}`);
+      console.error(
+        `[${(/* @__PURE__ */ new Date()).toISOString()}] syncFileAdd error for ${relativePath}: ${errMsg}`
+      );
     }
   }
   /**
@@ -8979,10 +8965,9 @@ var FileWatcher = class extends EventEmitter {
       [this.config.projectId, relativePath]
     );
     if (doc) {
-      run(
-        `UPDATE documents SET status = 'deleted', updated_at = datetime('now') WHERE id = ?`,
-        [doc.id]
-      );
+      run(`UPDATE documents SET status = 'deleted', updated_at = datetime('now') WHERE id = ?`, [
+        doc.id
+      ]);
     }
   }
   /**
@@ -9076,6 +9061,7 @@ var INITIAL_RETRY_DELAY_MS = 5e3;
 var DaemonManager = class extends EventEmitter2 {
   watchers = /* @__PURE__ */ new Map();
   watcherRetries = /* @__PURE__ */ new Map();
+  retryTimeouts = /* @__PURE__ */ new Map();
   running = false;
   startedAt = null;
   /**
@@ -9131,21 +9117,37 @@ var DaemonManager = class extends EventEmitter2 {
         if (currentRetries < MAX_WATCHER_RETRIES) {
           this.watcherRetries.set(project.key, currentRetries + 1);
           const delay = INITIAL_RETRY_DELAY_MS * Math.pow(2, currentRetries);
-          console.log(`[${(/* @__PURE__ */ new Date()).toISOString()}] [${project.key}] Will retry in ${delay}ms (attempt ${currentRetries + 1}/${MAX_WATCHER_RETRIES})`);
-          setTimeout(async () => {
+          console.log(
+            `[${(/* @__PURE__ */ new Date()).toISOString()}] [${project.key}] Will retry in ${delay}ms (attempt ${currentRetries + 1}/${MAX_WATCHER_RETRIES})`
+          );
+          const existingTimeout2 = this.retryTimeouts.get(project.key);
+          if (existingTimeout2) {
+            clearTimeout(existingTimeout2);
+          }
+          const timeout = setTimeout(async () => {
+            this.retryTimeouts.delete(project.key);
             if (this.running) {
               console.log(`[${(/* @__PURE__ */ new Date()).toISOString()}] [${project.key}] Attempting restart...`);
               await this.startWatcherWithRetry(project);
             }
           }, delay);
+          this.retryTimeouts.set(project.key, timeout);
         } else {
-          console.error(`[${(/* @__PURE__ */ new Date()).toISOString()}] [${project.key}] Max retries (${MAX_WATCHER_RETRIES}) exceeded - watcher disabled`);
+          console.error(
+            `[${(/* @__PURE__ */ new Date()).toISOString()}] [${project.key}] Max retries (${MAX_WATCHER_RETRIES}) exceeded - watcher disabled`
+          );
+          this.watcherRetries.delete(project.key);
           this.emit("watcherDisabled", { project: project.key });
         }
       });
       watcher.start();
       this.watchers.set(project.key, watcher);
-      this.watcherRetries.set(project.key, 0);
+      this.watcherRetries.delete(project.key);
+      const existingTimeout = this.retryTimeouts.get(project.key);
+      if (existingTimeout) {
+        clearTimeout(existingTimeout);
+        this.retryTimeouts.delete(project.key);
+      }
       console.log(`  \u2713 ${project.key}: ${project.path}`);
     } catch (error2) {
       console.error(`  \u2717 ${project.key}: Failed to start watcher - ${error2}`);
@@ -9153,12 +9155,22 @@ var DaemonManager = class extends EventEmitter2 {
       if (retryCount < MAX_WATCHER_RETRIES) {
         this.watcherRetries.set(project.key, retryCount + 1);
         const delay = INITIAL_RETRY_DELAY_MS * Math.pow(2, retryCount);
-        console.log(`[${(/* @__PURE__ */ new Date()).toISOString()}] [${project.key}] Will retry in ${delay}ms (attempt ${retryCount + 1}/${MAX_WATCHER_RETRIES})`);
-        setTimeout(async () => {
+        console.log(
+          `[${(/* @__PURE__ */ new Date()).toISOString()}] [${project.key}] Will retry in ${delay}ms (attempt ${retryCount + 1}/${MAX_WATCHER_RETRIES})`
+        );
+        const existingTimeout = this.retryTimeouts.get(project.key);
+        if (existingTimeout) {
+          clearTimeout(existingTimeout);
+        }
+        const timeout = setTimeout(async () => {
+          this.retryTimeouts.delete(project.key);
           if (this.running) {
             await this.startWatcherWithRetry(project);
           }
         }, delay);
+        this.retryTimeouts.set(project.key, timeout);
+      } else {
+        this.watcherRetries.delete(project.key);
       }
     }
   }
@@ -9170,6 +9182,11 @@ var DaemonManager = class extends EventEmitter2 {
       return;
     }
     console.log("Stopping all watchers...");
+    for (const [key, timeout] of this.retryTimeouts) {
+      clearTimeout(timeout);
+      console.log(`  \u2713 Cleared retry timeout: ${key}`);
+    }
+    this.retryTimeouts.clear();
     for (const [key, watcher] of this.watchers) {
       try {
         await watcher.stop();
@@ -9179,6 +9196,7 @@ var DaemonManager = class extends EventEmitter2 {
       }
     }
     this.watchers.clear();
+    this.watcherRetries.clear();
     this.running = false;
     this.startedAt = null;
     this.emit("stopped");
@@ -9295,7 +9313,7 @@ var DaemonManager = class extends EventEmitter2 {
    * Check if a project path is valid
    */
   isValidProject(path) {
-    return existsSync8(path) && existsSync8(join10(path, ".aigile"));
+    return existsSync10(path) && existsSync10(join11(path, ".aigile"));
   }
 };
 var daemonManagerInstance = null;
@@ -9318,29 +9336,29 @@ var DAEMON_NAME = "com.aigile.watcher";
 function getDaemonPaths() {
   const aigileHome = getAigileHome();
   const basePaths = {
-    pidFile: join11(aigileHome, "daemon.pid"),
-    logFile: join11(aigileHome, "daemon.log")
+    pidFile: join12(aigileHome, "daemon.pid"),
+    logFile: join12(aigileHome, "daemon.log")
   };
   if (PLATFORM === "darwin") {
     return {
       ...basePaths,
-      plist: join11(homedir2(), "Library", "LaunchAgents", `${DAEMON_NAME}.plist`)
+      plist: join12(homedir2(), "Library", "LaunchAgents", `${DAEMON_NAME}.plist`)
     };
   } else if (PLATFORM === "linux") {
     return {
       ...basePaths,
-      service: join11(homedir2(), ".config", "systemd", "user", `${DAEMON_NAME}.service`)
+      service: join12(homedir2(), ".config", "systemd", "user", `${DAEMON_NAME}.service`)
     };
   }
   return basePaths;
 }
 function isDaemonRunning() {
   const paths = getDaemonPaths();
-  if (!existsSync9(paths.pidFile)) {
+  if (!existsSync11(paths.pidFile)) {
     return { running: false };
   }
   try {
-    const pid = parseInt(readFileSync9(paths.pidFile, "utf-8").trim(), 10);
+    const pid = parseInt(readFileSync11(paths.pidFile, "utf-8").trim(), 10);
     try {
       process.kill(pid, 0);
       return { running: true, pid };
@@ -9354,12 +9372,12 @@ function isDaemonRunning() {
 }
 function writeCrashReport(error2) {
   try {
-    const crashDir = join11(getAigileHome(), CRASH_DIR_NAME);
-    if (!existsSync9(crashDir)) {
+    const crashDir = join12(getAigileHome(), CRASH_DIR_NAME);
+    if (!existsSync11(crashDir)) {
       mkdirSync5(crashDir, { recursive: true });
     }
     const timestamp = (/* @__PURE__ */ new Date()).toISOString().replace(/[:.]/g, "-");
-    const crashFile = join11(crashDir, `crash-${timestamp}.log`);
+    const crashFile = join12(crashDir, `crash-${timestamp}.log`);
     const report = [
       `AIGILE Daemon Crash Report`,
       `==========================`,
@@ -9372,7 +9390,7 @@ function writeCrashReport(error2) {
       `Error:`,
       error2 instanceof Error ? error2.stack || error2.message : String(error2)
     ].join("\n");
-    writeFileSync6(crashFile, report);
+    writeFileSync7(crashFile, report);
     console.error(`[${(/* @__PURE__ */ new Date()).toISOString()}] Crash report saved: ${crashFile}`);
     cleanupOldCrashReports(crashDir);
   } catch (writeErr) {
@@ -9381,7 +9399,7 @@ function writeCrashReport(error2) {
 }
 function cleanupOldCrashReports(crashDir) {
   try {
-    const files = readdirSync2(crashDir).filter((f) => f.startsWith("crash-") && f.endsWith(".log")).map((f) => ({ name: f, path: join11(crashDir, f) })).sort((a, b) => b.name.localeCompare(a.name));
+    const files = readdirSync3(crashDir).filter((f) => f.startsWith("crash-") && f.endsWith(".log")).map((f) => ({ name: f, path: join12(crashDir, f) })).sort((a, b) => b.name.localeCompare(a.name));
     for (let i = MAX_CRASH_REPORTS; i < files.length; i++) {
       try {
         unlinkSync(files[i].path);
@@ -9395,21 +9413,21 @@ function rotateLogIfNeeded() {
   const paths = getDaemonPaths();
   const logPath = paths.logFile;
   try {
-    if (!existsSync9(logPath)) return;
-    const stats = statSync3(logPath);
+    if (!existsSync11(logPath)) return;
+    const stats = statSync5(logPath);
     if (stats.size < MAX_LOG_SIZE) return;
     const timestamp = Date.now();
     const rotatedPath = `${logPath}.${timestamp}`;
     renameSync(logPath, rotatedPath);
     console.log(`[${(/* @__PURE__ */ new Date()).toISOString()}] Log rotated: ${rotatedPath}`);
-    cleanupOldLogs(dirname3(logPath));
+    cleanupOldLogs(dirname4(logPath));
   } catch (err) {
     console.error(`[${(/* @__PURE__ */ new Date()).toISOString()}] Log rotation error: ${err}`);
   }
 }
 function cleanupOldLogs(logDir) {
   try {
-    const files = readdirSync2(logDir).filter((f) => f.startsWith("daemon.log.")).map((f) => ({ name: f, path: join11(logDir, f) })).sort((a, b) => b.name.localeCompare(a.name));
+    const files = readdirSync3(logDir).filter((f) => f.startsWith("daemon.log.")).map((f) => ({ name: f, path: join12(logDir, f) })).sort((a, b) => b.name.localeCompare(a.name));
     for (let i = MAX_LOG_FILES; i < files.length; i++) {
       try {
         unlinkSync(files[i].path);
@@ -9423,7 +9441,7 @@ function cleanupOldLogs(logDir) {
 function generateLaunchAgentPlist() {
   const paths = getDaemonPaths();
   const nodePath = process.execPath;
-  const aigilePath = join11(dirname3(dirname3(import.meta.url.replace("file://", ""))), "bin", "aigile.js");
+  const aigilePath = join12(dirname4(dirname4(import.meta.url.replace("file://", ""))), "bin", "aigile.js");
   return `<?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
 <plist version="1.0">
@@ -9458,7 +9476,7 @@ function generateLaunchAgentPlist() {
 function generateSystemdService() {
   const paths = getDaemonPaths();
   const nodePath = process.execPath;
-  const aigilePath = join11(dirname3(dirname3(import.meta.url.replace("file://", ""))), "bin", "aigile.js");
+  const aigilePath = join12(dirname4(dirname4(import.meta.url.replace("file://", ""))), "bin", "aigile.js");
   return `[Unit]
 Description=AIGILE File Watcher Daemon
 After=network.target
@@ -9481,23 +9499,23 @@ daemonCommand.command("install").description("Install daemon to start automatica
   const opts = getOutputOptions(daemonCommand);
   const paths = getDaemonPaths();
   if (PLATFORM === "darwin") {
-    const plistDir = dirname3(paths.plist);
-    if (!existsSync9(plistDir)) {
+    const plistDir = dirname4(paths.plist);
+    if (!existsSync11(plistDir)) {
       mkdirSync5(plistDir, { recursive: true });
     }
     const plistContent = generateLaunchAgentPlist();
-    writeFileSync6(paths.plist, plistContent);
+    writeFileSync7(paths.plist, plistContent);
     success("Installed macOS LaunchAgent", opts);
     info(`Plist location: ${paths.plist}`, opts);
     info("Daemon will watch ALL registered projects", opts);
     info('Run "aigile daemon start" to start the watcher', opts);
   } else if (PLATFORM === "linux") {
-    const serviceDir = dirname3(paths.service);
-    if (!existsSync9(serviceDir)) {
+    const serviceDir = dirname4(paths.service);
+    if (!existsSync11(serviceDir)) {
       mkdirSync5(serviceDir, { recursive: true });
     }
     const serviceContent = generateSystemdService();
-    writeFileSync6(paths.service, serviceContent);
+    writeFileSync7(paths.service, serviceContent);
     try {
       execSync2("systemctl --user daemon-reload");
       execSync2(`systemctl --user enable ${DAEMON_NAME}`);
@@ -9506,7 +9524,7 @@ daemonCommand.command("install").description("Install daemon to start automatica
       info("Daemon will watch ALL registered projects", opts);
       info('Run "aigile daemon start" to start the watcher', opts);
     } catch (err) {
-      warning2("Service file created but could not enable. You may need to run:", opts);
+      warning("Service file created but could not enable. You may need to run:", opts);
       console.log(`  systemctl --user daemon-reload`);
       console.log(`  systemctl --user enable ${DAEMON_NAME}`);
     }
@@ -9527,14 +9545,14 @@ daemonCommand.command("uninstall").description("Remove daemon from auto-start").
     } catch {
     }
   }
-  if (PLATFORM === "darwin" && paths.plist && existsSync9(paths.plist)) {
+  if (PLATFORM === "darwin" && paths.plist && existsSync11(paths.plist)) {
     try {
       execSync2(`launchctl unload ${paths.plist}`);
     } catch {
     }
     unlinkSync(paths.plist);
     success("Removed macOS LaunchAgent", opts);
-  } else if (PLATFORM === "linux" && paths.service && existsSync9(paths.service)) {
+  } else if (PLATFORM === "linux" && paths.service && existsSync11(paths.service)) {
     try {
       execSync2(`systemctl --user stop ${DAEMON_NAME}`);
       execSync2(`systemctl --user disable ${DAEMON_NAME}`);
@@ -9549,7 +9567,7 @@ daemonCommand.command("uninstall").description("Remove daemon from auto-start").
   } else {
     info("No daemon installation found", opts);
   }
-  if (existsSync9(paths.pidFile)) {
+  if (existsSync11(paths.pidFile)) {
     unlinkSync(paths.pidFile);
   }
 });
@@ -9561,7 +9579,7 @@ daemonCommand.command("start").description("Start the file watcher daemon (watch
     info(`Daemon already running (PID: ${status.pid})`, opts);
     return;
   }
-  if (PLATFORM === "darwin" && paths.plist && existsSync9(paths.plist)) {
+  if (PLATFORM === "darwin" && paths.plist && existsSync11(paths.plist)) {
     try {
       execSync2(`launchctl load ${paths.plist}`);
       success("Started daemon via launchctl (watching all projects)", opts);
@@ -9569,7 +9587,7 @@ daemonCommand.command("start").description("Start the file watcher daemon (watch
       error("Failed to start daemon via launchctl", opts);
       process.exit(1);
     }
-  } else if (PLATFORM === "linux" && paths.service && existsSync9(paths.service)) {
+  } else if (PLATFORM === "linux" && paths.service && existsSync11(paths.service)) {
     try {
       execSync2(`systemctl --user start ${DAEMON_NAME}`);
       success("Started daemon via systemctl (watching all projects)", opts);
@@ -9586,7 +9604,7 @@ daemonCommand.command("start").description("Start the file watcher daemon (watch
     if (child.pid) {
       try {
         process.kill(child.pid, 0);
-        writeFileSync6(paths.pidFile, String(child.pid));
+        writeFileSync7(paths.pidFile, String(child.pid));
         success(`Started daemon (PID: ${child.pid}) - watching all projects`, opts);
       } catch {
         error("Failed to start daemon - process died immediately", opts);
@@ -9601,14 +9619,14 @@ daemonCommand.command("start").description("Start the file watcher daemon (watch
 daemonCommand.command("stop").description("Stop the file watcher daemon").action(() => {
   const opts = getOutputOptions(daemonCommand);
   const paths = getDaemonPaths();
-  if (PLATFORM === "darwin" && paths.plist && existsSync9(paths.plist)) {
+  if (PLATFORM === "darwin" && paths.plist && existsSync11(paths.plist)) {
     try {
       execSync2(`launchctl unload ${paths.plist}`);
       success("Stopped daemon via launchctl", opts);
     } catch {
       info("Daemon was not running", opts);
     }
-  } else if (PLATFORM === "linux" && paths.service && existsSync9(paths.service)) {
+  } else if (PLATFORM === "linux" && paths.service && existsSync11(paths.service)) {
     try {
       execSync2(`systemctl --user stop ${DAEMON_NAME}`);
       success("Stopped daemon via systemctl", opts);
@@ -9620,7 +9638,7 @@ daemonCommand.command("stop").description("Stop the file watcher daemon").action
     if (status.running && status.pid) {
       try {
         process.kill(status.pid, "SIGTERM");
-        if (existsSync9(paths.pidFile)) {
+        if (existsSync11(paths.pidFile)) {
           unlinkSync(paths.pidFile);
         }
         success(`Stopped daemon (PID: ${status.pid})`, opts);
@@ -9641,7 +9659,7 @@ daemonCommand.command("status").description("Show daemon status for ALL register
   const projectStats = [];
   let totalFiles = { allow: 0, unknown: 0, total: 0 };
   for (const project of projects) {
-    const valid = existsSync9(project.path) && existsSync9(join11(project.path, ".aigile"));
+    const valid = existsSync11(project.path) && existsSync11(join12(project.path, ".aigile"));
     const counts = queryAll(`
         SELECT COALESCE(monitoring_category, 'unknown') as monitoring_category, COUNT(*) as count
         FROM documents
@@ -9677,7 +9695,7 @@ daemonCommand.command("status").description("Show daemon status for ALL register
         running: status.running,
         pid: status.pid ?? null,
         platform: PLATFORM,
-        installed: PLATFORM === "darwin" ? paths.plist && existsSync9(paths.plist) : PLATFORM === "linux" ? paths.service && existsSync9(paths.service) : false,
+        installed: PLATFORM === "darwin" ? paths.plist && existsSync11(paths.plist) : PLATFORM === "linux" ? paths.service && existsSync11(paths.service) : false,
         projectCount: projects.length,
         validProjectCount: validCount,
         projects: projectStats,
@@ -9694,7 +9712,7 @@ daemonCommand.command("status").description("Show daemon status for ALL register
   console.log("\n\u{1F4CA} Daemon Status\n");
   console.log(`\u251C\u2500\u2500 Running: ${status.running ? "\u2705 Yes" : "\u274C No"}${status.pid ? ` (PID: ${status.pid})` : ""}`);
   console.log(`\u251C\u2500\u2500 Platform: ${PLATFORM}`);
-  const installed = PLATFORM === "darwin" ? paths.plist && existsSync9(paths.plist) : PLATFORM === "linux" ? paths.service && existsSync9(paths.service) : false;
+  const installed = PLATFORM === "darwin" ? paths.plist && existsSync11(paths.plist) : PLATFORM === "linux" ? paths.service && existsSync11(paths.service) : false;
   console.log(`\u251C\u2500\u2500 Installed: ${installed ? "\u2705 Yes" : "\u274C No"}`);
   console.log(`\u251C\u2500\u2500 Projects: ${validCount}/${projects.length} valid`);
   if (projectStats.length > 0) {
@@ -9742,7 +9760,7 @@ daemonCommand.command("run").option("--skip-resync", "Skip initial resync on sta
     console.error(`[${(/* @__PURE__ */ new Date()).toISOString()}] FATAL: Uncaught exception:`);
     console.error(err.stack || err.message);
     writeCrashReport(err);
-    if (existsSync9(paths.pidFile)) {
+    if (existsSync11(paths.pidFile)) {
       try {
         unlinkSync(paths.pidFile);
       } catch {
@@ -9754,7 +9772,7 @@ daemonCommand.command("run").option("--skip-resync", "Skip initial resync on sta
     console.error(`[${(/* @__PURE__ */ new Date()).toISOString()}] FATAL: Unhandled promise rejection:`);
     console.error(reason);
     writeCrashReport(reason);
-    if (existsSync9(paths.pidFile)) {
+    if (existsSync11(paths.pidFile)) {
       try {
         unlinkSync(paths.pidFile);
       } catch {
@@ -9763,7 +9781,7 @@ daemonCommand.command("run").option("--skip-resync", "Skip initial resync on sta
     process.exit(1);
   });
   rotateLogIfNeeded();
-  writeFileSync6(paths.pidFile, String(process.pid));
+  writeFileSync7(paths.pidFile, String(process.pid));
   console.log(`[${(/* @__PURE__ */ new Date()).toISOString()}] Starting AIGILE daemon for all registered projects...`);
   console.log(`[${(/* @__PURE__ */ new Date()).toISOString()}] PID: ${process.pid}, Node: ${process.version}, Platform: ${platform()}`);
   const manager = getDaemonManager();
@@ -9794,7 +9812,7 @@ daemonCommand.command("run").option("--skip-resync", "Skip initial resync on sta
     console.log(`[${(/* @__PURE__ */ new Date()).toISOString()}] Shutting down...`);
     const forceExitTimeout = setTimeout(() => {
       console.error(`[${(/* @__PURE__ */ new Date()).toISOString()}] Shutdown timeout (${SHUTDOWN_TIMEOUT_MS}ms) - forcing exit`);
-      if (existsSync9(paths.pidFile)) {
+      if (existsSync11(paths.pidFile)) {
         try {
           unlinkSync(paths.pidFile);
         } catch {
@@ -9808,7 +9826,7 @@ daemonCommand.command("run").option("--skip-resync", "Skip initial resync on sta
       console.error(`[${(/* @__PURE__ */ new Date()).toISOString()}] Error during shutdown: ${err}`);
     }
     clearTimeout(forceExitTimeout);
-    if (existsSync9(paths.pidFile)) {
+    if (existsSync11(paths.pidFile)) {
       unlinkSync(paths.pidFile);
     }
     console.log(`[${(/* @__PURE__ */ new Date()).toISOString()}] Daemon stopped gracefully`);
@@ -9832,7 +9850,7 @@ daemonCommand.command("run").option("--skip-resync", "Skip initial resync on sta
     }
   } catch (err) {
     console.error(`[${(/* @__PURE__ */ new Date()).toISOString()}] Failed to start daemon: ${err}`);
-    if (existsSync9(paths.pidFile)) {
+    if (existsSync11(paths.pidFile)) {
       unlinkSync(paths.pidFile);
     }
     process.exit(1);
@@ -9841,7 +9859,7 @@ daemonCommand.command("run").option("--skip-resync", "Skip initial resync on sta
 daemonCommand.command("logs").option("-n, --lines <number>", "Number of lines to show", "50").option("-f, --follow", "Follow log output").description("Show daemon logs").action((options) => {
   const opts = getOutputOptions(daemonCommand);
   const paths = getDaemonPaths();
-  if (!existsSync9(paths.logFile)) {
+  if (!existsSync11(paths.logFile)) {
     info("No log file found. Daemon may not have run yet.", opts);
     return;
   }
@@ -10000,11 +10018,13 @@ function formatBytes(bytes) {
 init_connection();
 init_connection();
 import { Command as Command21 } from "commander";
-import { readFileSync as readFileSync10, existsSync as existsSync10 } from "fs";
-import { join as join12, relative as relative4 } from "path";
+import { readFileSync as readFileSync12, existsSync as existsSync12 } from "fs";
+import { join as join13, relative as relative6 } from "path";
 import { glob } from "glob";
 init_config();
-var fileCommand = new Command21("file").description("Shadow mode file analysis and management for brownfield projects");
+var fileCommand = new Command21("file").description(
+  "Shadow mode file analysis and management for brownfield projects"
+);
 function getProjectContext(opts) {
   const projectRoot = findProjectRoot();
   if (!projectRoot) {
@@ -10016,10 +10036,9 @@ function getProjectContext(opts) {
     error("Could not load project config.", opts);
     return null;
   }
-  const project = queryOne(
-    "SELECT id FROM projects WHERE key = ?",
-    [config.project.key]
-  );
+  const project = queryOne("SELECT id FROM projects WHERE key = ?", [
+    config.project.key
+  ]);
   if (!project) {
     error(`Project "${config.project.key}" not found in database.`, opts);
     return null;
@@ -10042,12 +10061,15 @@ fileCommand.command("analyze <path>").option("--tldr <tldr>", "One-line summary
   if (!ctx) {
     process.exit(1);
   }
-  const normalizedPath = filePath.startsWith("/") ? relative4(ctx.projectRoot, filePath) : filePath;
+  const normalizedPath = filePath.startsWith("/") ? relative6(ctx.projectRoot, filePath) : filePath;
   const doc = getDocumentWithAnalysis(ctx.projectId, normalizedPath);
   if (!doc) {
     const tracked = trackShadowFile(ctx.projectId, ctx.projectRoot, normalizedPath);
     if (!tracked) {
-      error(`File not tracked. Run "aigile sync scan" or track with "aigile file track ${normalizedPath}"`, opts);
+      error(
+        `File not tracked. Run "aigile sync scan" or track with "aigile file track ${normalizedPath}"`,
+        opts
+      );
       process.exit(1);
     }
   }
@@ -10072,24 +10094,26 @@ fileCommand.command("analyze <path>").option("--tldr <tldr>", "One-line summary
   }
   const updatedDoc = getDocumentWithAnalysis(ctx.projectId, normalizedPath);
   if (opts.json) {
-    console.log(JSON.stringify({
-      success: true,
-      data: {
-        path: normalizedPath,
-        analyzed: true,
-        analyzedAt: updatedDoc?.analyzed_at,
-        metadata: {
-          tldr: updatedDoc?.meta_tldr,
-          module: updatedDoc?.inferred_module,
-          component: updatedDoc?.inferred_component,
-          type: updatedDoc?.file_type,
-          dependencies: updatedDoc?.meta_dependencies ? JSON.parse(updatedDoc.meta_dependencies) : null,
-          exports: updatedDoc?.exports ? JSON.parse(updatedDoc.exports) : null,
-          complexity: updatedDoc?.complexity_score,
-          confidence: updatedDoc?.analysis_confidence
+    console.log(
+      JSON.stringify({
+        success: true,
+        data: {
+          path: normalizedPath,
+          analyzed: true,
+          analyzedAt: updatedDoc?.analyzed_at,
+          metadata: {
+            tldr: updatedDoc?.meta_tldr,
+            module: updatedDoc?.inferred_module,
+            component: updatedDoc?.inferred_component,
+            type: updatedDoc?.file_type,
+            dependencies: updatedDoc?.meta_dependencies ? JSON.parse(updatedDoc.meta_dependencies) : null,
+            exports: updatedDoc?.exports ? JSON.parse(updatedDoc.exports) : null,
+            complexity: updatedDoc?.complexity_score,
+            confidence: updatedDoc?.analysis_confidence
+          }
         }
-      }
-    }));
+      })
+    );
   } else {
     success(`Analysis added for: ${normalizedPath}`, opts);
     if (updatedDoc?.meta_tldr) {
@@ -10138,24 +10162,26 @@ fileCommand.command("list").alias("ls").option("--unanalyzed", "Only files witho
     documents = getUnanalyzedDocuments(ctx.projectId, limit, offset);
   }
   if (opts.json || options.format === "json") {
-    console.log(JSON.stringify({
-      success: true,
-      data: documents.map((d) => ({
-        path: d.path,
-        filename: d.filename,
-        extension: d.extension,
-        module: d.inferred_module,
-        component: d.inferred_component,
-        fileType: d.file_type,
-        analyzed: !!d.analyzed_at,
-        analyzedAt: d.analyzed_at,
-        confidence: d.analysis_confidence,
-        tldr: d.meta_tldr,
-        dependencies: d.meta_dependencies ? JSON.parse(d.meta_dependencies) : null,
-        exports: d.exports ? JSON.parse(d.exports) : null,
-        complexity: d.complexity_score
-      }))
-    }));
+    console.log(
+      JSON.stringify({
+        success: true,
+        data: documents.map((d) => ({
+          path: d.path,
+          filename: d.filename,
+          extension: d.extension,
+          module: d.inferred_module,
+          component: d.inferred_component,
+          fileType: d.file_type,
+          analyzed: !!d.analyzed_at,
+          analyzedAt: d.analyzed_at,
+          confidence: d.analysis_confidence,
+          tldr: d.meta_tldr,
+          dependencies: d.meta_dependencies ? JSON.parse(d.meta_dependencies) : null,
+          exports: d.exports ? JSON.parse(d.exports) : null,
+          complexity: d.complexity_score
+        }))
+      })
+    );
   } else if (options.format === "paths") {
     documents.forEach((d) => console.log(d.path));
   } else {
@@ -10214,15 +10240,15 @@ fileCommand.command("read <path>").option("--with-metadata", "Include existing D
   if (!ctx) {
     process.exit(1);
   }
-  const normalizedPath = filePath.startsWith("/") ? relative4(ctx.projectRoot, filePath) : filePath;
-  const fullPath = join12(ctx.projectRoot, normalizedPath);
-  if (!existsSync10(fullPath)) {
+  const normalizedPath = filePath.startsWith("/") ? relative6(ctx.projectRoot, filePath) : filePath;
+  const fullPath = join13(ctx.projectRoot, normalizedPath);
+  if (!existsSync12(fullPath)) {
     error(`File not found: ${normalizedPath}`, opts);
     process.exit(1);
   }
   let content;
   try {
-    content = readFileSync10(fullPath, "utf-8");
+    content = readFileSync12(fullPath, "utf-8");
   } catch {
     error(`Could not read file: ${normalizedPath}`, opts);
     process.exit(1);
@@ -10236,22 +10262,24 @@ fileCommand.command("read <path>").option("--with-metadata", "Include existing D
     lines = lines.slice(0, options.limit);
   }
   if (opts.json) {
-    console.log(JSON.stringify({
-      success: true,
-      data: {
-        path: normalizedPath,
-        content: lines.join("\n"),
-        lineCount: lines.length,
-        metadata: metadata ? {
-          tldr: metadata.meta_tldr,
-          module: metadata.inferred_module,
-          component: metadata.inferred_component,
-          fileType: metadata.file_type,
-          analyzed: !!metadata.analyzed_at,
-          confidence: metadata.analysis_confidence
-        } : null
-      }
-    }));
+    console.log(
+      JSON.stringify({
+        success: true,
+        data: {
+          path: normalizedPath,
+          content: lines.join("\n"),
+          lineCount: lines.length,
+          metadata: metadata ? {
+            tldr: metadata.meta_tldr,
+            module: metadata.inferred_module,
+            component: metadata.inferred_component,
+            fileType: metadata.file_type,
+            analyzed: !!metadata.analyzed_at,
+            confidence: metadata.analysis_confidence
+          } : null
+        }
+      })
+    );
   } else {
     if (options.withMetadata && metadata) {
       console.log(`# File: ${normalizedPath}`);
@@ -10275,7 +10303,7 @@ fileCommand.command("track <path>").option("--type <type>", "File type classific
   if (!ctx) {
     process.exit(1);
   }
-  const normalizedPath = filePath.startsWith("/") ? relative4(ctx.projectRoot, filePath) : filePath;
+  const normalizedPath = filePath.startsWith("/") ? relative6(ctx.projectRoot, filePath) : filePath;
   const tracked = trackShadowFile(ctx.projectId, ctx.projectRoot, normalizedPath);
   if (!tracked) {
     error(`Could not track file: ${normalizedPath}`, opts);
@@ -10290,18 +10318,20 @@ fileCommand.command("track <path>").option("--type <type>", "File type classific
   }
   const doc = getDocumentWithAnalysis(ctx.projectId, normalizedPath);
   if (opts.json) {
-    console.log(JSON.stringify({
-      success: true,
-      data: {
-        path: normalizedPath,
-        tracked: true,
-        shadowMode: true,
-        metadata: doc ? {
-          fileType: doc.file_type,
-          module: doc.inferred_module
-        } : null
-      }
-    }));
+    console.log(
+      JSON.stringify({
+        success: true,
+        data: {
+          path: normalizedPath,
+          tracked: true,
+          shadowMode: true,
+          metadata: doc ? {
+            fileType: doc.file_type,
+            module: doc.inferred_module
+          } : null
+        }
+      })
+    );
   } else {
     success(`Tracked in shadow mode: ${normalizedPath}`, opts);
   }
@@ -10312,39 +10342,41 @@ fileCommand.command("show <path>").description("Show detailed file analysis").ac
   if (!ctx) {
     process.exit(1);
   }
-  const normalizedPath = filePath.startsWith("/") ? relative4(ctx.projectRoot, filePath) : filePath;
+  const normalizedPath = filePath.startsWith("/") ? relative6(ctx.projectRoot, filePath) : filePath;
   const doc = getDocumentWithAnalysis(ctx.projectId, normalizedPath);
   if (!doc) {
     error(`File not tracked: ${normalizedPath}`, opts);
     process.exit(1);
   }
   if (opts.json) {
-    console.log(JSON.stringify({
-      success: true,
-      data: {
-        path: doc.path,
-        filename: doc.filename,
-        extension: doc.extension,
-        status: doc.status,
-        sizeBytes: doc.size_bytes,
-        lastScanned: doc.last_scanned_at,
-        hasFrontmatter: !!doc.has_frontmatter,
-        shadowMode: !!doc.shadow_mode,
-        analysis: {
-          analyzed: !!doc.analyzed_at,
-          analyzedAt: doc.analyzed_at,
-          confidence: doc.analysis_confidence,
-          tldr: doc.meta_tldr,
-          module: doc.inferred_module,
-          component: doc.inferred_component,
-          fileType: doc.file_type,
-          complexity: doc.complexity_score,
-          dependencies: doc.meta_dependencies ? JSON.parse(doc.meta_dependencies) : null,
-          exports: doc.exports ? JSON.parse(doc.exports) : null,
-          notes: doc.analysis_notes
+    console.log(
+      JSON.stringify({
+        success: true,
+        data: {
+          path: doc.path,
+          filename: doc.filename,
+          extension: doc.extension,
+          status: doc.status,
+          sizeBytes: doc.size_bytes,
+          lastScanned: doc.last_scanned_at,
+          hasFrontmatter: !!doc.has_frontmatter,
+          shadowMode: !!doc.shadow_mode,
+          analysis: {
+            analyzed: !!doc.analyzed_at,
+            analyzedAt: doc.analyzed_at,
+            confidence: doc.analysis_confidence,
+            tldr: doc.meta_tldr,
+            module: doc.inferred_module,
+            component: doc.inferred_component,
+            fileType: doc.file_type,
+            complexity: doc.complexity_score,
+            dependencies: doc.meta_dependencies ? JSON.parse(doc.meta_dependencies) : null,
+            exports: doc.exports ? JSON.parse(doc.exports) : null,
+            notes: doc.analysis_notes
+          }
         }
-      }
-    }));
+      })
+    );
   } else {
     const displayData = {
       path: doc.path,
@@ -10403,8 +10435,8 @@ fileCommand.command("tag").argument("<path>", "File path to tag").option("--chun
     error('No active session. Start one with "aigile session start".', opts);
     process.exit(1);
   }
-  const normalizedPath = filePath.startsWith("/") ? relative4(ctx.projectRoot, filePath) : filePath;
-  const doc = queryOne(
+  const normalizedPath = filePath.startsWith("/") ? relative6(ctx.projectRoot, filePath) : filePath;
+  let doc = queryOne(
     "SELECT id FROM documents WHERE project_id = ? AND path = ?",
     [ctx.projectId, normalizedPath]
   );
@@ -10422,7 +10454,7 @@ fileCommand.command("tag").argument("<path>", "File path to tag").option("--chun
       error(`Could not track file: ${normalizedPath}`, opts);
       process.exit(1);
     }
-    doc.id = newDoc.id;
+    doc = newDoc;
   }
   const validTypes = ["assigned", "explored", "skipped"];
   if (!validTypes.includes(options.type)) {
@@ -10437,17 +10469,19 @@ fileCommand.command("tag").argument("<path>", "File path to tag").option("--chun
     isFoundational: options.foundational ?? false
   });
   if (opts.json) {
-    console.log(JSON.stringify({
-      success: true,
-      data: {
-        session_file_id: sessionFileId,
-        path: normalizedPath,
-        session_id: session.id,
-        chunk_id: options.chunk ?? null,
-        review_type: options.type,
-        is_foundational: options.foundational ?? false
-      }
-    }));
+    console.log(
+      JSON.stringify({
+        success: true,
+        data: {
+          session_file_id: sessionFileId,
+          path: normalizedPath,
+          session_id: session.id,
+          chunk_id: options.chunk ?? null,
+          review_type: options.type,
+          is_foundational: options.foundational ?? false
+        }
+      })
+    );
   } else {
     success(`Tagged: ${normalizedPath}`, opts);
     if (options.chunk) {
@@ -10470,7 +10504,7 @@ fileCommand.command("tag-batch").option("--chunk <id>", "Chunk ID for all files"
   let filesToTag = [];
   if (options.glob) {
     const matches = await glob(options.glob, { cwd: ctx.projectRoot, nodir: true });
-    filesToTag = matches.map((f) => relative4(ctx.projectRoot, join12(ctx.projectRoot, f)));
+    filesToTag = matches.map((f) => relative6(ctx.projectRoot, join13(ctx.projectRoot, f)));
   } else {
     error("Please provide --glob pattern. Stdin not supported yet.", opts);
     process.exit(1);
@@ -10499,10 +10533,12 @@ fileCommand.command("tag-batch").option("--chunk <id>", "Chunk ID for all files"
     tagged++;
   }
   if (opts.json) {
-    console.log(JSON.stringify({
-      success: true,
-      data: { tagged, skipped, total: filesToTag.length }
-    }));
+    console.log(
+      JSON.stringify({
+        success: true,
+        data: { tagged, skipped, total: filesToTag.length }
+      })
+    );
   } else {
     success(`Tagged ${tagged} files (${skipped} skipped - not tracked)`, opts);
   }
@@ -10538,12 +10574,14 @@ fileCommand.command("untag").argument("<path>", "File path to untag").option("--
     warning(`File "${filePath}" is not tagged in this session.`, opts);
     return;
   }
-  queryOne("DELETE FROM session_files WHERE id = ?", [existing.id]);
+  run("DELETE FROM session_files WHERE id = ?", [existing.id]);
   if (opts.json) {
-    console.log(JSON.stringify({
-      success: true,
-      data: { path: filePath, untagged: true }
-    }));
+    console.log(
+      JSON.stringify({
+        success: true,
+        data: { path: filePath, untagged: true }
+      })
+    );
   } else {
     success(`Untagged: ${filePath}`, opts);
   }
@@ -10586,12 +10624,14 @@ fileCommand.command("clear-tags").option("--session <id>", "Session ID (default:
     deleteQuery += " AND chunk_id = ?";
     deleteParams.push(options.chunk);
   }
-  queryOne(deleteQuery, deleteParams);
+  run(deleteQuery, deleteParams);
   if (opts.json) {
-    console.log(JSON.stringify({
-      success: true,
-      data: { session_id: sessionId, cleared: count }
-    }));
+    console.log(
+      JSON.stringify({
+        success: true,
+        data: { session_id: sessionId, cleared: count }
+      })
+    );
   } else {
     success(`Cleared ${count} tag(s)`, opts);
   }
@@ -10616,15 +10656,17 @@ fileCommand.command("untagged").option("--session <id>", "Session ID (default: c
     assignedOnly: options.assignedOnly
   });
   if (opts.json) {
-    console.log(JSON.stringify({
-      success: true,
-      data: {
-        session_id: sessionId,
-        chunk_id: options.chunk ?? null,
-        count: untagged.length,
-        files: untagged.map((f) => f.path)
-      }
-    }));
+    console.log(
+      JSON.stringify({
+        success: true,
+        data: {
+          session_id: sessionId,
+          chunk_id: options.chunk ?? null,
+          count: untagged.length,
+          files: untagged.map((f) => f.path)
+        }
+      })
+    );
   } else {
     if (untagged.length === 0) {
       success("All files have been tagged!", opts);
@@ -10692,22 +10734,24 @@ fileCommand.command("coverage").option("--session <id>", "Session ID (default: c
     const total = totalTagged + untagged.length;
     const pct = total > 0 ? Math.round(totalTagged / total * 100) : 100;
     if (opts.json) {
-      console.log(JSON.stringify({
-        success: true,
-        data: {
-          session_id: sessionId,
-          total_files: total,
-          tagged: totalTagged,
-          untagged: untagged.length,
-          coverage_percent: pct,
-          by_type: {
-            assigned: stats.assigned.reviewed,
-            explored: stats.explored,
-            foundational: stats.foundational,
-            skipped: stats.skipped
+      console.log(
+        JSON.stringify({
+          success: true,
+          data: {
+            session_id: sessionId,
+            total_files: total,
+            tagged: totalTagged,
+            untagged: untagged.length,
+            coverage_percent: pct,
+            by_type: {
+              assigned: stats.assigned.reviewed,
+              explored: stats.explored,
+              foundational: stats.foundational,
+              skipped: stats.skipped
+            }
           }
-        }
-      }));
+        })
+      );
     } else {
       console.log(`
 Coverage for session ${sessionId.slice(0, 8)}...`);
@@ -10734,7 +10778,7 @@ fileCommand.command("flag").argument("<path>", "File path to flag").option("--du
     error('No active session. Start one with "aigile session start".', opts);
     process.exit(1);
   }
-  const normalizedPath = filePath.startsWith("/") ? relative4(ctx.projectRoot, filePath) : filePath;
+  const normalizedPath = filePath.startsWith("/") ? relative6(ctx.projectRoot, filePath) : filePath;
   const sessionFile = queryOne(
     `SELECT sf.id FROM session_files sf
        JOIN documents d ON sf.document_id = d.id
@@ -10742,7 +10786,10 @@ fileCommand.command("flag").argument("<path>", "File path to flag").option("--du
     [session.id, normalizedPath]
   );
   if (!sessionFile) {
-    error(`File not tagged in this session: ${normalizedPath}. Tag it first with "aigile file tag".`, opts);
+    error(
+      `File not tagged in this session: ${normalizedPath}. Tag it first with "aigile file tag".`,
+      opts
+    );
     process.exit(1);
   }
   const issues = [];
@@ -10761,13 +10808,15 @@ fileCommand.command("flag").argument("<path>", "File path to flag").option("--du
   }
   flagFileQualityIssue(sessionFile.id, issues);
   if (opts.json) {
-    console.log(JSON.stringify({
-      success: true,
-      data: {
-        path: normalizedPath,
-        issues
-      }
-    }));
+    console.log(
+      JSON.stringify({
+        success: true,
+        data: {
+          path: normalizedPath,
+          issues
+        }
+      })
+    );
   } else {
     success(`Flagged: ${normalizedPath}`, opts);
     for (const issue of issues) {
@@ -10795,10 +10844,9 @@ fileCommand.command("duplicates").option("--session <id>", "Session ID (default:
   for (const sf of filesWithIssues) {
     if (!sf.quality_issues) continue;
     const issues = JSON.parse(sf.quality_issues);
-    const doc = queryOne(
-      "SELECT path FROM documents WHERE id = ?",
-      [sf.document_id]
-    );
+    const doc = queryOne("SELECT path FROM documents WHERE id = ?", [
+      sf.document_id
+    ]);
     if (!doc) continue;
     for (const issue of issues) {
       if (issue.startsWith("duplicate:")) {
@@ -10813,10 +10861,12 @@ fileCommand.command("duplicates").option("--session <id>", "Session ID (default:
     }
   }
   if (opts.json) {
-    console.log(JSON.stringify({
-      success: true,
-      data: { duplicates }
-    }));
+    console.log(
+      JSON.stringify({
+        success: true,
+        data: { duplicates }
+      })
+    );
   } else {
     if (duplicates.length === 0) {
       info("No duplicates flagged.", opts);
@@ -10853,10 +10903,9 @@ fileCommand.command("issues").option("--session <id>", "Session ID (default: cur
   }
   const issueList = [];
   for (const sf of filesWithIssues) {
-    const doc = queryOne(
-      "SELECT path FROM documents WHERE id = ?",
-      [sf.document_id]
-    );
+    const doc = queryOne("SELECT path FROM documents WHERE id = ?", [
+      sf.document_id
+    ]);
     if (!doc) continue;
     issueList.push({
       path: doc.path,
@@ -10864,10 +10913,12 @@ fileCommand.command("issues").option("--session <id>", "Session ID (default: cur
     });
   }
   if (opts.json) {
-    console.log(JSON.stringify({
-      success: true,
-      data: { files_with_issues: issueList }
-    }));
+    console.log(
+      JSON.stringify({
+        success: true,
+        data: { files_with_issues: issueList }
+      })
+    );
   } else {
     console.log(`Files with quality issues (${issueList.length}):`);
     for (const file of issueList) {
@@ -10885,7 +10936,7 @@ init_connection();
 init_connection();
 import { Command as Command22 } from "commander";
 import { glob as glob2 } from "glob";
-import { relative as relative5, resolve as resolve2 } from "path";
+import { relative as relative7, resolve as resolve5 } from "path";
 init_config();
 function safeParseArray(json) {
   if (!json) return [];
@@ -10932,7 +10983,7 @@ chunkCommand.command("create").argument("<id>", "Chunk ID (e.g., chunk-001)").op
   if (options.pattern) {
     for (const pattern of options.pattern) {
       const matches = await glob2(pattern, { cwd: projectRoot, nodir: true });
-      assignedFiles.push(...matches.map((f) => relative5(projectRoot, resolve2(projectRoot, f))));
+      assignedFiles.push(...matches.map((f) => relative7(projectRoot, resolve5(projectRoot, f))));
     }
   }
   if (options.assign) {
@@ -11046,12 +11097,12 @@ chunkCommand.command("list").alias("ls").description("List all chunks in current
   }
   const session = getActiveSession(project.id);
   if (!session) {
-    warning2("No active session.", opts);
+    warning("No active session.", opts);
     return;
   }
   const chunks = getSessionChunks(session.id);
   if (chunks.length === 0) {
-    warning2("No chunks defined in current session.", opts);
+    warning("No chunks defined in current session.", opts);
     return;
   }
   data(