@noyrax/5d-database-plugin 0.1.14-beta.1 → 0.1.14-beta.11

package/out/cli/debug-plugin-id.js

@@ -0,0 +1,188 @@
+#!/usr/bin/env node
+"use strict";
+/**
+ * Debug Tool: Plugin ID Verification
+ *
+ * Verifies plugin ID calculation and checks database for matching plugin IDs.
+ * Useful for debugging foreign system issues where plugin IDs don't match.
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+const path = __importStar(require("path"));
+const crypto = __importStar(require("crypto"));
+const sqlite3 = __importStar(require("sqlite3"));
+const fs = __importStar(require("fs"));
+/**
+ * Calculates plugin ID using the same method as MultiDbManager.
+ */
+function calculatePluginId(workspaceRoot) {
+    const normalizedPath = path.resolve(workspaceRoot).replace(/\\/g, '/').toLowerCase();
+    const hash = crypto.createHash('sha256').update(normalizedPath).digest('hex');
+    return hash.substring(0, 16);
+}
+/**
+ * Gets all unique plugin IDs from a database.
+ */
+function getPluginIdsFromDatabase(dbPath, tableName) {
+    return new Promise((resolve, reject) => {
+        if (!fs.existsSync(dbPath)) {
+            resolve([]);
+            return;
+        }
+        const db = new sqlite3.Database(dbPath, sqlite3.OPEN_READONLY, (err) => {
+            if (err) {
+                reject(err);
+                return;
+            }
+        });
+        db.all(`SELECT DISTINCT plugin_id FROM ${tableName} WHERE plugin_id IS NOT NULL`, [], (err, rows) => {
+            db.close();
+            if (err) {
+                reject(err);
+            }
+            else {
+                resolve(rows.map(r => r.plugin_id));
+            }
+        });
+    });
+}
+/**
+ * Main debug function.
+ */
+async function debugPluginId(workspaceRoot) {
+    console.log('=== Plugin ID Debug Tool ===\n');
+    console.log(`Workspace Root: ${workspaceRoot}\n`);
+    // 1. Calculate plugin ID
+    const calculatedPluginId = calculatePluginId(workspaceRoot);
+    const normalizedPath = path.resolve(workspaceRoot).replace(/\\/g, '/').toLowerCase();
+    console.log('1. Plugin ID Calculation:');
+    console.log(`   Normalized Path: ${normalizedPath}`);
+    console.log(`   Calculated Plugin ID: ${calculatedPluginId}\n`);
+    // 2. Check databases
+    const dbDirectory = path.join(workspaceRoot, '.database-plugin');
+    if (!fs.existsSync(dbDirectory)) {
+        console.log('2. Database Directory:');
+        console.log(`   ❌ Not found: ${dbDirectory}`);
+        console.log(`   → Run ingestion first: noyrax-5d-database ingest <workspace-root>`);
+        return;
+    }
+    console.log('2. Database Plugin IDs:');
+    const dbFiles = [
+        { file: 'modules.db', table: 'modules', name: 'X (Modules)' },
+        { file: 'symbols.db', table: 'symbols', name: 'Y (Symbols)' },
+        { file: 'dependencies.db', table: 'dependencies', name: 'Z (Dependencies)' },
+        { file: 'adrs.db', table: 'adrs', name: 'W (ADRs)' },
+        { file: 'changes.db', table: 'change_reports', name: 'T (Changes)' }
+    ];
+    const allPluginIds = new Set();
+    for (const { file, table, name } of dbFiles) {
+        const dbPath = path.join(dbDirectory, file);
+        try {
+            const pluginIds = await getPluginIdsFromDatabase(dbPath, table);
+            console.log(`   ${name}:`);
+            if (pluginIds.length === 0) {
+                console.log(`      ⚠️  No plugin IDs found (database empty or table doesn't exist)`);
+            }
+            else {
+                pluginIds.forEach(id => {
+                    allPluginIds.add(id);
+                    const match = id === calculatedPluginId;
+                    console.log(`      ${match ? '✅' : '❌'} ${id} ${match ? '(MATCH)' : '(MISMATCH)'}`);
+                });
+            }
+        }
+        catch (error) {
+            console.log(`   ${name}:`);
+            console.log(`      ❌ Error: ${error.message}`);
+        }
+    }
+    console.log('\n3. Summary:');
+    if (allPluginIds.size === 0) {
+        console.log('   ⚠️  No plugin IDs found in databases');
+        console.log('   → Run ingestion first: noyrax-5d-database ingest <workspace-root>');
+    }
+    else if (allPluginIds.has(calculatedPluginId)) {
+        console.log(`   ✅ Plugin ID matches: ${calculatedPluginId}`);
+        console.log('   → All queries should work correctly');
+    }
+    else {
+        console.log(`   ❌ Plugin ID mismatch!`);
+        console.log(`   → Calculated: ${calculatedPluginId}`);
+        console.log(`   → In Database: ${Array.from(allPluginIds).join(', ')}`);
+        console.log('\n   Possible causes:');
+        console.log('   1. Workspace root changed after ingestion');
+        console.log('   2. Ingestion was run with different workspace root');
+        console.log('   3. Plugin ID calculation method changed');
+        console.log('\n   Solution:');
+        console.log('   → Re-run ingestion with current workspace root:');
+        console.log(`     noyrax-5d-database ingest "${workspaceRoot}" --full`);
+    }
+    console.log('\n4. Verification Query:');
+    const modulesDb = path.join(dbDirectory, 'modules.db');
+    if (fs.existsSync(modulesDb)) {
+        try {
+            const db = new sqlite3.Database(modulesDb, sqlite3.OPEN_READONLY);
+            db.get(`SELECT COUNT(*) as count FROM modules WHERE plugin_id = ?`, [calculatedPluginId], (err, row) => {
+                db.close();
+                if (err) {
+                    console.log(`   ❌ Error: ${err.message}`);
+                }
+                else {
+                    const count = row?.count || 0;
+                    console.log(`   Modules with calculated Plugin ID: ${count}`);
+                    if (count === 0) {
+                        console.log('   ⚠️  No modules found with calculated Plugin ID');
+                    }
+                    else {
+                        console.log(`   ✅ Found ${count} module(s) with matching Plugin ID`);
+                    }
+                }
+            });
+        }
+        catch (error) {
+            console.log(`   ❌ Error: ${error.message}`);
+        }
+    }
+    else {
+        console.log('   ⚠️  modules.db not found');
+    }
+}
+// CLI entry point
+const workspaceRoot = process.argv[2] || process.cwd();
+debugPluginId(workspaceRoot).catch(error => {
+    console.error('Error:', error);
+    process.exit(1);
+});
+//# sourceMappingURL=debug-plugin-id.js.map

package/out/cli/debug-plugin-id.js.map

@@ -0,0 +1 @@
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package/out/cli/ingest-cli.js

@@ -107,32 +107,43 @@ function loadEnvFile(workspaceRoot) {
 }
 /**
  * CLI tool for ingesting documentation into the 5D database.
- * Usage: node ingest-cli.js <workspace-root> [--full]
+ * Usage: node ingest-cli.js <workspace-root> [--full] [--cleanup]
  */
 async function main() {
     const args = process.argv.slice(2);
     // Auto-detect workspace root if not provided
     let workspaceRoot;
     let isFull;
+    let shouldCleanup;
     if (args.length === 0) {
         // No arguments: use current working directory
         workspaceRoot = process.cwd();
         isFull = false;
+        shouldCleanup = false;
     }
     else if (args[0] === '--full') {
         // First arg is --full: use current working directory
         workspaceRoot = process.cwd();
         isFull = true;
+        shouldCleanup = args.includes('--cleanup');
     }
-    else if (args.includes('--full')) {
-        // Workspace root provided, --full flag present
+    else if (args[0] === '--cleanup') {
+        // First arg is --cleanup: use current working directory
+        workspaceRoot = process.cwd();
+        isFull = args.includes('--full');
+        shouldCleanup = true;
+    }
+    else if (args.includes('--full') || args.includes('--cleanup')) {
+        // Workspace root provided, flags present
         workspaceRoot = path.resolve(args[0]);
-        isFull = true;
+        isFull = args.includes('--full');
+        shouldCleanup = args.includes('--cleanup');
     }
     else {
-        // Workspace root provided, no --full flag
+        // Workspace root provided, no flags
         workspaceRoot = path.resolve(args[0]);
         isFull = false;
+        shouldCleanup = false;
     }
     // Load .env file from workspace root or parent directories
     loadEnvFile(workspaceRoot);
@@ -144,6 +155,9 @@ async function main() {
     }
     console.log(`Ingesting documentation from: ${workspaceRoot}`);
     console.log(`Mode: ${isFull ? 'full' : 'incremental'}`);
+    if (shouldCleanup) {
+        console.log(`Cleanup: enabled (will delete old databases with different plugin ID)`);
+    }
     // Find docs directory (dependency on Documentation System Plugin)
     const docsPath = docs_path_resolver_1.DocsPathResolver.findDocsDirectoryFromPath(workspaceRoot);
     if (!docsPath) {
@@ -164,6 +178,31 @@ async function main() {
     const dbManager = new multi_db_manager_1.MultiDbManager(workspaceRoot);
     const pluginRoot = path.resolve(__dirname, '..', '..');
     const migrationManager = new migration_manager_1.MigrationManager(dbManager, pluginRoot);
+    // Check for plugin ID mismatch
+    const hasMismatch = await dbManager.checkPluginIdMismatch();
+    if (hasMismatch) {
+        if (shouldCleanup || isFull) {
+            // Automatic cleanup on --cleanup flag or --full ingestion
+            if (isFull) {
+                console.log(`[Ingest CLI] Plugin ID mismatch detected. Automatically cleaning up old databases (--full mode).`);
+            }
+            else {
+                console.log(`[Ingest CLI] Plugin ID mismatch detected. Cleaning up old databases (--cleanup flag).`);
+            }
+            await dbManager.cleanupOldDatabases();
+        }
+        else {
+            console.error(`[Ingest CLI] ERROR: Plugin ID mismatch detected!`);
+            console.error(`[Ingest CLI] Current plugin ID: ${dbManager.getPluginId()}`);
+            console.error(`[Ingest CLI] Old databases have a different plugin ID (workspace may have been moved/renamed).`);
+            console.error(`[Ingest CLI]`);
+            console.error(`[Ingest CLI] Solution: Run ingestion with --cleanup flag to delete old databases:`);
+            console.error(`[Ingest CLI]   noyrax-5d-database ingest "${workspaceRoot}" --cleanup`);
+            console.error(`[Ingest CLI] Or use --full flag (automatically cleans up):`);
+            console.error(`[Ingest CLI]   noyrax-5d-database ingest "${workspaceRoot}" --full`);
+            process.exit(1);
+        }
+    }
     // Validate that required documentation files exist (hard validation - exits on failure)
     validateWorkspaceRoot(workspaceRoot, docsPath);
     const ingestionOrchestrator = new ingestion_orchestrator_1.IngestionOrchestrator(dbManager, migrationManager, docsPath);

package/out/cli/ingest-cli.js.map

@@ -1 +1 @@
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package/out/cli/tool-cli.js

@@ -107,7 +107,7 @@ async function main() {
         console.error('  system_explanation                 - Get system overview');
         console.error('  learning_path <topic>              - Generate learning path');
         console.error('  cross_analysis <filePath>          - Cross-dimension analysis');
-        console.error('  gap_analysis [--min-deps N] [--limit N] [--auto-generate] - Find documentation gaps (--auto-generate: automatically generate ADRs)');
+        console.error('  gap_analysis [--min-deps N] [--limit N] [--auto-generate] - Find documentation gaps (--auto-generate: optional, default: false. When false, provides context_for_adr_generation for KI-Agent)');
         console.error('  architecture_mining [filePath]      - Mine architectural decisions from code');
         console.error('  adr_generator [--min-deps N] [--limit N] [--dry-run] [--use-llm] [--llm-model MODEL] - Reconstruct ADRs from 5D dimensions (--use-llm: use LLM for "Why" reconstruction)');
         process.exit(1);

package/out/cli/tool-cli.js.map

@@ -1 +1 @@
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package/out/core/chromadb-vector-database.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"chromadb-vector-database.d.ts","sourceRoot":"","sources":["../../src/core/chromadb-vector-database.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,OAAO,MAAM,SAAS,CAAC;AAGnC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAG7D;;;;;;GAMG;AACH,qBAAa,sBAAuB,YAAW,cAAc;IACzD,OAAO,CAAC,EAAE,CAAmB;IAC7B,OAAO,CAAC,aAAa,CAAS;IAC9B,OAAO,CAAC,YAAY,CAAoB;IACxC,OAAO,CAAC,UAAU,CAAoB;IACtC,OAAO,CAAC,SAAS,CAAkB;IACnC,OAAO,CAAC,QAAQ,CAAC,mBAAmB,CAAgB;IACpD,OAAO,CAAC,QAAQ,CAAC,cAAc,CAAwB;gBAE3C,EAAE,EAAE,OAAO,CAAC,QAAQ,EAAE,aAAa,EAAE,MAAM;IAKvD;;OAEG;IACH,WAAW,IAAI,OAAO;IAItB;;OAEG;IACG,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;IA6DjC;;OAEG;IACG,eAAe,CAAC,WAAW,EAAE,MAAM,EAAE,eAAe,EAAE,YAAY,GAAG,MAAM,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC;IAwCnG;;OAEG;IACG,MAAM,CACR,cAAc,EAAE,YAAY,GAAG,MAAM,EAAE,EACvC,KAAK,EAAE,MAAM,EACb,SAAS,CAAC,EAAE,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,EACvC,QAAQ,CAAC,EAAE,MAAM,GAClB,OAAO,CAAC,KAAK,CAAC;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,MAAM,CAAC;QAAC,UAAU,CAAC,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IAuE3E;;OAEG;IACG,uBAAuB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC;IAgBpE;;OAEG;YACW,uBAAuB;IAgBrC;;OAEG;YACW,gBAAgB;CAejC"}

package/out/core/chromadb-vector-database.js

@@ -70,15 +70,13 @@ class ChromaDbVectorDatabase {
                 const chromadb = require('chromadb');
                 ChromaClient = chromadb.ChromaClient;
                 if (!ChromaClient) {
-                    console.warn('[ChromaDbVectorDatabase] ChromaClient not found in chromadb package.');
+                    // Removed console.warn to prevent stdout interference with MCP JSON-RPC protocol
                     this.available = false;
                     return;
                 }
             }
             catch (importError) {
-                console.warn('[ChromaDbVectorDatabase] chromadb package not found.');
-                console.warn('[ChromaDbVectorDatabase] Please install chromadb: npm install chromadb');
-                console.warn('[ChromaDbVectorDatabase] For now, falling back to cosine similarity.');
+                // Removed console.warn to prevent stdout interference with MCP JSON-RPC protocol
                 this.available = false;
                 return;
             }
@@ -92,10 +90,10 @@ class ChromaDbVectorDatabase {
                     host: 'localhost',
                     port: 8000
                 });
-                console.log(`[ChromaDbVectorDatabase] Initialized ChromaDB client (server: localhost:8000)`);
+                // Removed console.log to prevent stdout interference with MCP JSON-RPC protocol
             }
             catch (serverError) {
-                console.warn(`[ChromaDbVectorDatabase] Failed to initialize ChromaDB client: ${serverError}`);
+                // Removed console.warn to prevent stdout interference with MCP JSON-RPC protocol
                 this.available = false;
                 return;
             }
@@ -112,15 +110,15 @@ class ChromaDbVectorDatabase {
                     }
                 });
                 this.available = true;
-                console.log('[ChromaDbVectorDatabase] ChromaDB initialized successfully.');
+                // Removed console.log to prevent stdout interference with MCP JSON-RPC protocol
             }
             catch (collectionError) {
-                console.warn(`[ChromaDbVectorDatabase] Failed to get/create collection: ${collectionError}`);
+                // Removed console.warn to prevent stdout interference with MCP JSON-RPC protocol
                 this.available = false;
             }
         }
         catch (error) {
-            console.warn(`[ChromaDbVectorDatabase] Initialization failed: ${error}`);
+            // Removed console.warn to prevent stdout interference with MCP JSON-RPC protocol
             this.available = false;
         }
     }
@@ -144,7 +142,7 @@ class ChromaDbVectorDatabase {
             // We need to query by ID directly since we don't have pluginId here
             const embedding = await this.getEmbeddingById(embeddingId);
             if (!embedding) {
-                console.warn(`[ChromaDbVectorDatabase] Embedding ${embeddingId} not found in embeddings table`);
+                // Removed console.warn to prevent stdout interference with MCP JSON-RPC protocol
                 return;
             }
             // Upsert to ChromaDB
@@ -161,7 +159,7 @@ class ChromaDbVectorDatabase {
             });
         }
         catch (error) {
-            console.warn(`[ChromaDbVectorDatabase] Failed to upsert embedding: ${error}`);
+            // Removed console.warn to prevent stdout interference with MCP JSON-RPC protocol
         }
     }
     /**
@@ -226,7 +224,7 @@ class ChromaDbVectorDatabase {
             return mappedResults;
         }
         catch (error) {
-            console.warn(`[ChromaDbVectorDatabase] Search failed: ${error}`);
+            // Removed console.warn to prevent stdout interference with MCP JSON-RPC protocol
             return [];
         }
     }

package/out/core/chromadb-vector-database.js.map

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package/out/core/migration-manager.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"migration-manager.d.ts","sourceRoot":"","sources":["../../src/core/migration-manager.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,cAAc,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAC;AAW/D;;;GAGG;AACH,qBAAa,gBAAgB;IACzB,OAAO,CAAC,SAAS,CAAiB;IAClC,OAAO,CAAC,mBAAmB,CAAS;IAEpC;;;;;OAKG;gBACS,SAAS,EAAE,cAAc,EAAE,UAAU,EAAE,MAAM;IAKzD;;;;;OAKG;YACW,6BAA6B;IAkD3C;;;;;;;OAOG;YACW,qBAAqB;IAoDnC;;;;;OAKG;YACW,oBAAoB;IAclC;;;;;;OAMG;IACH;;;;;;;OAOG;YACW,oBAAoB;IAclC;;;;;OAKG;IACH,OAAO,CAAC,iBAAiB;IAQzB;;;;;;;;OAQG;YACW,cAAc;IAiC5B;;;;;OAKG;IACH,OAAO,CAAC,6BAA6B;IAgBrC;;;;;OAKG;IACH,OAAO,CAAC,kBAAkB;IAY1B;;;;;OAKG;IACH,OAAO,CAAC,iBAAiB;IAYzB;;;;;;OAMG;YACW,gBAAgB;IAuB9B;;;;;OAKG;IACU,OAAO,CAAC,SAAS,EAAE,SAAS,GAAG,OAAO,CAAC,IAAI,CAAC;IA2EzD;;;;OAIG;IACU,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;CAM3C"}
+{"version":3,"file":"migration-manager.d.ts","sourceRoot":"","sources":["../../src/core/migration-manager.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,cAAc,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAC;AAW/D;;;GAGG;AACH,qBAAa,gBAAgB;IACzB,OAAO,CAAC,SAAS,CAAiB;IAClC,OAAO,CAAC,mBAAmB,CAAS;IAEpC;;;;;OAKG;gBACS,SAAS,EAAE,cAAc,EAAE,UAAU,EAAE,MAAM;IAKzD;;;;;OAKG;YACW,6BAA6B;IAkD3C;;;;;;;OAOG;YACW,qBAAqB;IAoDnC;;;;;OAKG;YACW,oBAAoB;IAclC;;;;;;OAMG;IACH;;;;;;;OAOG;YACW,oBAAoB;IAclC;;;;;OAKG;IACH,OAAO,CAAC,iBAAiB;IAQzB;;;;;;;;OAQG;YACW,cAAc;IAwC5B;;;;;OAKG;IACH,OAAO,CAAC,6BAA6B;IAuCrC;;;;;OAKG;IACH,OAAO,CAAC,kBAAkB;IAY1B;;;;;OAKG;IACH,OAAO,CAAC,iBAAiB;IAYzB;;;;;;OAMG;YACW,gBAAgB;IAuB9B;;;;;OAKG;IACU,OAAO,CAAC,SAAS,EAAE,SAAS,GAAG,OAAO,CAAC,IAAI,CAAC;IA2EzD;;;;OAIG;IACU,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;CAM3C"}

package/out/core/migration-manager.js

@@ -116,13 +116,13 @@ class MigrationManager {
                         return;
                     }
                     // Create table with new structure
-                    db.run(`
-                        CREATE TABLE migrations (
-                            version INTEGER NOT NULL,
-                            name TEXT NOT NULL,
-                            applied_at DATETIME DEFAULT CURRENT_TIMESTAMP,
-                            PRIMARY KEY (version, name)
-                        )
+                    db.run(`
+                        CREATE TABLE migrations (
+                            version INTEGER NOT NULL,
+                            name TEXT NOT NULL,
+                            applied_at DATETIME DEFAULT CURRENT_TIMESTAMP,
+                            PRIMARY KEY (version, name)
+                        )
                     `, (createErr) => {
                         if (createErr) {
                             reject(createErr);
@@ -136,13 +136,13 @@ class MigrationManager {
         }
         // Table doesn't exist or has correct structure - create if not exists
         return new Promise((resolve, reject) => {
-            db.run(`
-                CREATE TABLE IF NOT EXISTS migrations (
-                    version INTEGER NOT NULL,
-                    name TEXT NOT NULL,
-                    applied_at DATETIME DEFAULT CURRENT_TIMESTAMP,
-                    PRIMARY KEY (version, name)
-                )
+            db.run(`
+                CREATE TABLE IF NOT EXISTS migrations (
+                    version INTEGER NOT NULL,
+                    name TEXT NOT NULL,
+                    applied_at DATETIME DEFAULT CURRENT_TIMESTAMP,
+                    PRIMARY KEY (version, name)
+                )
             `, (err) => {
                 if (err) {
                     reject(err);
@@ -228,27 +228,34 @@ class MigrationManager {
         return new Promise((resolve, reject) => {
             db.exec(sql, (err) => {
                 if (err) {
-                    reject(new Error(`Failed to apply migration ${version}_${name}: ${err.message}`));
+                    // Ignore "duplicate column" errors - columns may already exist from previous migrations
+                    // This can happen when migrations are split or renamed
+                    if (err.message.includes('duplicate column')) {
+                        console.log(`[MigrationManager] Migration ${version}_${name}: Column already exists, skipping: ${err.message}`);
+                        // Continue to insert migration record even if column already exists
+                    }
+                    else {
+                        reject(new Error(`Failed to apply migration ${version}_${name}: ${err.message}`));
+                        return;
+                    }
                 }
-                else {
-                    // Use INSERT OR IGNORE to handle race conditions
-                    // If migration already exists, it will be silently ignored
-                    db.run('INSERT OR IGNORE INTO migrations (version, name) VALUES (?, ?)', [version, name], (insertErr) => {
-                        if (insertErr) {
-                            // If it's a UNIQUE constraint error, migration already exists - that's OK
-                            if (insertErr.message.includes('UNIQUE constraint')) {
-                                console.log(`[MigrationManager] Migration ${version}_${name} already exists, skipping insert`);
-                                resolve();
-                            }
-                            else {
-                                reject(insertErr);
-                            }
+                // Use INSERT OR IGNORE to handle race conditions
+                // If migration already exists, it will be silently ignored
+                db.run('INSERT OR IGNORE INTO migrations (version, name) VALUES (?, ?)', [version, name], (insertErr) => {
+                    if (insertErr) {
+                        // If it's a UNIQUE constraint error, migration already exists - that's OK
+                        if (insertErr.message.includes('UNIQUE constraint')) {
+                            console.log(`[MigrationManager] Migration ${version}_${name} already exists, skipping insert`);
+                            resolve();
                         }
                         else {
-                            resolve();
+                            reject(insertErr);
                         }
-                    });
-                }
+                    }
+                    else {
+                        resolve();
+                    }
+                });
             });
         });
     }
@@ -268,7 +275,29 @@ class MigrationManager {
             const dimensionPrefix = this.getDimensionPrefix(dimension);
             return file.startsWith(dimensionPrefix);
         })
-            .sort();
+            .sort((a, b) => {
+            // Extract version number
+            const versionMatchA = a.match(/^(\d+)_/);
+            const versionMatchB = b.match(/^(\d+)_/);
+            if (!versionMatchA || !versionMatchB) {
+                return a.localeCompare(b);
+            }
+            const versionA = parseInt(versionMatchA[1], 10);
+            const versionB = parseInt(versionMatchB[1], 10);
+            // Sort by version first
+            if (versionA !== versionB) {
+                return versionA - versionB;
+            }
+            // For same version, prioritize "initial_" migrations
+            const isInitialA = a.includes('_initial_');
+            const isInitialB = b.includes('_initial_');
+            if (isInitialA && !isInitialB)
+                return -1;
+            if (!isInitialA && isInitialB)
+                return 1;
+            // Otherwise, sort alphabetically
+            return a.localeCompare(b);
+        });
         return files;
     }
     /**