@mduenas/codegraph 0.5.6 → 0.6.0

package/README.md

@@ -596,7 +596,7 @@ The `.codegraph/config.json` file controls indexing behavior:
 | Ruby | `.rb` | Full support |
 | C | `.c`, `.h` | Full support |
 | C++ | `.cpp`, `.hpp`, `.cc` | Full support |
-| Swift | `.swift` | Basic support |
+| Swift | `.swift` | Full support |
 | Kotlin | `.kt`, `.kts` | Full support |
 
 ## 🔧 Troubleshooting

package/dist/bin/codegraph.js

@@ -689,11 +689,12 @@ function main() {
                 // Server will run until terminated
             }
             else {
-                // Default: show info about MCP mode
-                console.log(chalk.bold('\nCodeGraph MCP Server\n'));
-                info('Use --mcp flag to start the MCP server');
-                console.log('\nTo use with Claude Code, add to your MCP configuration:');
-                console.log(chalk.dim(`
+                // Default: show info about MCP mode.
+                // Use stderr so stdout stays clean for any piped/stdio usage.
+                console.error(chalk.bold('\nCodeGraph MCP Server\n'));
+                console.error(chalk.blue('ℹ') + ' Use --mcp flag to start the MCP server');
+                console.error('\nTo use with Claude Code, add to your MCP configuration:');
+                console.error(chalk.dim(`
 {
   "mcpServers": {
     "codegraph": {
@@ -703,8 +704,8 @@ function main() {
   }
 }
 `));
-                console.log('\nTo use with GitHub Copilot (.copilot/mcp-config.json):');
-                console.log(chalk.dim(`
+                console.error('\nTo use with GitHub Copilot (.copilot/mcp-config.json):');
+                console.error(chalk.dim(`
 {
   "mcpServers": {
     "codegraph": {
@@ -716,14 +717,14 @@ function main() {
   }
 }
 `));
-                console.log('Available tools:');
-                console.log(chalk.cyan('  codegraph_search') + '    - Search for code symbols');
-                console.log(chalk.cyan('  codegraph_context') + '   - Build context for a task');
-                console.log(chalk.cyan('  codegraph_callers') + '   - Find callers of a symbol');
-                console.log(chalk.cyan('  codegraph_callees') + '   - Find what a symbol calls');
-                console.log(chalk.cyan('  codegraph_impact') + '    - Analyze impact of changes');
-                console.log(chalk.cyan('  codegraph_node') + '      - Get symbol details');
-                console.log(chalk.cyan('  codegraph_status') + '    - Get index status');
+                console.error('Available tools:');
+                console.error(chalk.cyan('  codegraph_search') + '    - Search for code symbols');
+                console.error(chalk.cyan('  codegraph_context') + '   - Build context for a task');
+                console.error(chalk.cyan('  codegraph_callers') + '   - Find callers of a symbol');
+                console.error(chalk.cyan('  codegraph_callees') + '   - Find what a symbol calls');
+                console.error(chalk.cyan('  codegraph_impact') + '    - Analyze impact of changes');
+                console.error(chalk.cyan('  codegraph_node') + '      - Get symbol details');
+                console.error(chalk.cyan('  codegraph_status') + '    - Get index status');
             }
         }
         catch (err) {

package/dist/bin/codegraph.js.map

@@ -1 +1 @@
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package/dist/config.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAIH,OAAO,EAAE,eAAe,EAA4B,QAAQ,EAAE,MAAM,SAAS,CAAC;AAE9E;;GAEG;AACH,eAAO,MAAM,eAAe,gBAAgB,CAAC;AAE7C;;GAEG;AACH,wBAAgB,aAAa,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAEzD;AAED;;GAEG;AACH,wBAAgB,cAAc,CAAC,MAAM,EAAE,OAAO,GAAG,MAAM,IAAI,eAAe,CAuDzE;AAwBD;;GAEG;AACH,wBAAgB,UAAU,CAAC,WAAW,EAAE,MAAM,GAAG,eAAe,CA8B/D;AAED;;GAEG;AACH,wBAAgB,UAAU,CAAC,WAAW,EAAE,MAAM,EAAE,MAAM,EAAE,eAAe,GAAG,IAAI,CAe7E;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,WAAW,EAAE,MAAM,GAAG,eAAe,CAKxE;AAED;;GAEG;AACH,wBAAgB,YAAY,CAC1B,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE,OAAO,CAAC,eAAe,CAAC,GAChC,eAAe,CAMjB;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,eAAe,CAM3F;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,eAAe,CAM3F;AAED;;GAEG;AACH,wBAAgB,gBAAgB,CAC9B,WAAW,EAAE,MAAM,EACnB,IAAI,EAAE,MAAM,EACZ,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,QAAQ,GACb,eAAe,CAkBjB;AAED;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,eAAe,GAAG,OAAO,CA+BpF"}
+{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAIH,OAAO,EAAE,eAAe,EAA4B,QAAQ,EAAE,MAAM,SAAS,CAAC;AAE9E;;GAEG;AACH,eAAO,MAAM,eAAe,gBAAgB,CAAC;AAE7C;;GAEG;AACH,wBAAgB,aAAa,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAEzD;AAED;;GAEG;AACH,wBAAgB,cAAc,CAAC,MAAM,EAAE,OAAO,GAAG,MAAM,IAAI,eAAe,CAuDzE;AAwBD;;GAEG;AACH,wBAAgB,UAAU,CAAC,WAAW,EAAE,MAAM,GAAG,eAAe,CA8B/D;AAED;;GAEG;AACH,wBAAgB,UAAU,CAAC,WAAW,EAAE,MAAM,EAAE,MAAM,EAAE,eAAe,GAAG,IAAI,CAmB7E;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,WAAW,EAAE,MAAM,GAAG,eAAe,CAKxE;AAED;;GAEG;AACH,wBAAgB,YAAY,CAC1B,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE,OAAO,CAAC,eAAe,CAAC,GAChC,eAAe,CAMjB;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,eAAe,CAM3F;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,eAAe,CAM3F;AAED;;GAEG;AACH,wBAAgB,gBAAgB,CAC9B,WAAW,EAAE,MAAM,EACnB,IAAI,EAAE,MAAM,EACZ,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,QAAQ,GACb,eAAe,CAkBjB;AAED;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,eAAe,GAAG,OAAO,CA+BpF"}

package/dist/config.js

@@ -196,7 +196,10 @@ function saveConfig(projectRoot, config) {
     const toSave = { ...config };
     delete toSave.rootDir;
     const content = JSON.stringify(toSave, null, 2);
-    fs.writeFileSync(configPath, content, 'utf-8');
+    // Atomic write: write to temp file then rename to prevent partial/corrupt configs
+    const tmpPath = configPath + '.tmp';
+    fs.writeFileSync(tmpPath, content, 'utf-8');
+    fs.renameSync(tmpPath, configPath);
 }
 /**
  * Create default configuration for a new project

package/dist/config.js.map

@@ -1 +1 @@
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package/dist/context/index.d.ts.map

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package/dist/context/index.js

@@ -42,9 +42,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.formatContextAsJson = exports.formatContextAsMarkdown = exports.ContextBuilder = void 0;
 exports.createContextBuilder = createContextBuilder;
 const fs = __importStar(require("fs"));
-const path = __importStar(require("path"));
 const formatter_1 = require("./formatter");
 const errors_1 = require("../errors");
+const utils_1 = require("../utils");
 /**
  * Default options for context building
  *
@@ -284,8 +284,8 @@ class ContextBuilder {
      * Extract code from a node's source file
      */
     async extractNodeCode(node) {
-        const filePath = path.join(this.projectRoot, node.filePath);
-        if (!fs.existsSync(filePath)) {
+        const filePath = (0, utils_1.validatePathWithinRoot)(this.projectRoot, node.filePath);
+        if (!filePath || !fs.existsSync(filePath)) {
             return null;
         }
         try {

package/dist/context/index.js.map

@@ -1 +1 @@
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package/dist/db/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/db/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,QAAQ,MAAM,gBAAgB,CAAC;AAGtC,OAAO,EAAE,aAAa,EAAE,MAAM,UAAU,CAAC;AAGzC;;GAEG;AACH,qBAAa,kBAAkB;IAC7B,OAAO,CAAC,EAAE,CAAoB;IAC9B,OAAO,CAAC,MAAM,CAAS;IAEvB,OAAO;IAKP;;OAEG;IACH,MAAM,CAAC,UAAU,CAAC,MAAM,EAAE,MAAM,GAAG,kBAAkB;IA2BrD;;OAEG;IACH,MAAM,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,GAAG,kBAAkB;IA2B/C;;OAEG;IACH,KAAK,IAAI,QAAQ,CAAC,QAAQ;IAI1B;;OAEG;IACH,OAAO,IAAI,MAAM;IAIjB;;OAEG;IACH,gBAAgB,IAAI,aAAa,GAAG,IAAI;IAcxC;;OAEG;IACH,WAAW,CAAC,CAAC,EAAE,EAAE,EAAE,MAAM,CAAC,GAAG,CAAC;IAI9B;;OAEG;IACH,OAAO,IAAI,MAAM;IAKjB;;OAEG;IACH,QAAQ,IAAI,IAAI;IAKhB;;OAEG;IACH,KAAK,IAAI,IAAI;IAIb;;OAEG;IACH,MAAM,IAAI,OAAO;CAGlB;AAED;;GAEG;AACH,eAAO,MAAM,iBAAiB,iBAAiB,CAAC;AAEhD;;GAEG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAE3D"}

package/dist/db/index.js

@@ -71,6 +71,11 @@ class DatabaseConnection {
         // Enable foreign keys and WAL mode for better performance
         db.pragma('foreign_keys = ON');
         db.pragma('journal_mode = WAL');
+        // Performance tuning
+        db.pragma('synchronous = NORMAL'); // Safe with WAL mode
+        db.pragma('cache_size = -64000'); // 64 MB page cache
+        db.pragma('temp_store = MEMORY'); // Temp tables in memory
+        db.pragma('mmap_size = 268435456'); // 256 MB memory-mapped I/O
         // Run schema initialization
         const schemaPath = path.join(__dirname, 'schema.sql');
         const schema = fs.readFileSync(schemaPath, 'utf-8');
@@ -88,6 +93,11 @@ class DatabaseConnection {
         // Enable foreign keys and WAL mode
         db.pragma('foreign_keys = ON');
         db.pragma('journal_mode = WAL');
+        // Performance tuning
+        db.pragma('synchronous = NORMAL');
+        db.pragma('cache_size = -64000');
+        db.pragma('temp_store = MEMORY');
+        db.pragma('mmap_size = 268435456');
         // Check and run migrations if needed
         const conn = new DatabaseConnection(db, dbPath);
         const currentVersion = (0, migrations_1.getCurrentVersion)(db);

package/dist/db/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/db/index.ts"],"names":[],"mappings":";AAAA;;;;GAIG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAmJH,0CAEC;AAnJD,oEAAsC;AACtC,uCAAyB;AACzB,2CAA6B;AAE7B,6CAAwF;AAExF;;GAEG;AACH,MAAa,kBAAkB;IACrB,EAAE,CAAoB;IACtB,MAAM,CAAS;IAEvB,YAAoB,EAAqB,EAAE,MAAc;QACvD,IAAI,CAAC,EAAE,GAAG,EAAE,CAAC;QACb,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC;IACvB,CAAC;IAED;;OAEG;IACH,MAAM,CAAC,UAAU,CAAC,MAAc;QAC9B,iCAAiC;QACjC,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC;QACjC,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YACxB,EAAE,CAAC,SAAS,CAAC,GAAG,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QACzC,CAAC;QAED,gCAAgC;QAChC,MAAM,EAAE,GAAG,IAAI,wBAAQ,CAAC,MAAM,CAAC,CAAC;QAEhC,0DAA0D;QAC1D,EAAE,CAAC,MAAM,CAAC,mBAAmB,CAAC,CAAC;QAC/B,EAAE,CAAC,MAAM,CAAC,oBAAoB,CAAC,CAAC;QAEhC,4BAA4B;QAC5B,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,YAAY,CAAC,CAAC;QACtD,MAAM,MAAM,GAAG,EAAE,CAAC,YAAY,CAAC,UAAU,EAAE,OAAO,CAAC,CAAC;QACpD,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QAEhB,OAAO,IAAI,kBAAkB,CAAC,EAAE,EAAE,MAAM,CAAC,CAAC;IAC5C,CAAC;IAED;;OAEG;IACH,MAAM,CAAC,IAAI,CAAC,MAAc;QACxB,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,MAAM,CAAC,EAAE,CAAC;YAC3B,MAAM,IAAI,KAAK,CAAC,uBAAuB,MAAM,EAAE,CAAC,CAAC;QACnD,CAAC;QAED,MAAM,EAAE,GAAG,IAAI,wBAAQ,CAAC,MAAM,CAAC,CAAC;QAEhC,mCAAmC;QACnC,EAAE,CAAC,MAAM,CAAC,mBAAmB,CAAC,CAAC;QAC/B,EAAE,CAAC,MAAM,CAAC,oBAAoB,CAAC,CAAC;QAEhC,qCAAqC;QACrC,MAAM,IAAI,GAAG,IAAI,kBAAkB,CAAC,EAAE,EAAE,MAAM,CAAC,CAAC;QAChD,MAAM,cAAc,GAAG,IAAA,8BAAiB,EAAC,EAAE,CAAC,CAAC;QAE7C,IAAI,cAAc,GAAG,mCAAsB,EAAE,CAAC;YAC5C,IAAA,0BAAa,EAAC,EAAE,EAAE,cAAc,CAAC,CAAC;QACpC,CAAC;QAED,OAAO,IAAI,CAAC;IACd,CAAC;IAED;;OAEG;IACH,KAAK;QACH,OAAO,IAAI,CAAC,EAAE,CAAC;IACjB,CAAC;IAED;;OAEG;IACH,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC;IACrB,CAAC;IAED;;OAEG;IACH,gBAAgB;QACd,MAAM,GAAG,GAAG,IAAI,CAAC,EAAE;aAChB,OAAO,CAAC,4FAA4F,CAAC;aACrG,GAAG,EAAqF,CAAC;QAE5F,IAAI,CAAC,GAAG;YAAE,OAAO,IAAI,CAAC;QAEtB,OAAO;YACL,OAAO,EAAE,GAAG,CAAC,OAAO;YACpB,SAAS,EAAE,GAAG,CAAC,UAAU;YACzB,WAAW,EAAE,GAAG,CAAC,WAAW,IAAI,SAAS;SAC1C,CAAC;IACJ,CAAC;IAED;;OAEG;IACH,WAAW,CAAI,EAAW;QACxB,OAAO,IAAI,CAAC,EAAE,CAAC,WAAW,CAAC,EAAE,CAAC,EAAE,CAAC;IACnC,CAAC;IAED;;OAEG;IACH,OAAO;QACL,MAAM,KAAK,GAAG,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QACvC,OAAO,KAAK,CAAC,IAAI,CAAC;IACpB,CAAC;IAED;;OAEG;IACH,QAAQ;QACN,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;QACvB,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;IAC1B,CAAC;IAED;;OAEG;IACH,KAAK;QACH,IAAI,CAAC,EAAE,CAAC,KAAK,EAAE,CAAC;IAClB,CAAC;IAED;;OAEG;IACH,MAAM;QACJ,OAAO,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC;IACtB,CAAC;CACF;AA9HD,gDA8HC;AAED;;GAEG;AACU,QAAA,iBAAiB,GAAG,cAAc,CAAC;AAEhD;;GAEG;AACH,SAAgB,eAAe,CAAC,WAAmB;IACjD,OAAO,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,YAAY,EAAE,yBAAiB,CAAC,CAAC;AACjE,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/db/index.ts"],"names":[],"mappings":";AAAA;;;;GAIG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AA6JH,0CAEC;AA7JD,oEAAsC;AACtC,uCAAyB;AACzB,2CAA6B;AAE7B,6CAAwF;AAExF;;GAEG;AACH,MAAa,kBAAkB;IACrB,EAAE,CAAoB;IACtB,MAAM,CAAS;IAEvB,YAAoB,EAAqB,EAAE,MAAc;QACvD,IAAI,CAAC,EAAE,GAAG,EAAE,CAAC;QACb,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC;IACvB,CAAC;IAED;;OAEG;IACH,MAAM,CAAC,UAAU,CAAC,MAAc;QAC9B,iCAAiC;QACjC,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC;QACjC,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YACxB,EAAE,CAAC,SAAS,CAAC,GAAG,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QACzC,CAAC;QAED,gCAAgC;QAChC,MAAM,EAAE,GAAG,IAAI,wBAAQ,CAAC,MAAM,CAAC,CAAC;QAEhC,0DAA0D;QAC1D,EAAE,CAAC,MAAM,CAAC,mBAAmB,CAAC,CAAC;QAC/B,EAAE,CAAC,MAAM,CAAC,oBAAoB,CAAC,CAAC;QAChC,qBAAqB;QACrB,EAAE,CAAC,MAAM,CAAC,sBAAsB,CAAC,CAAC,CAAK,qBAAqB;QAC5D,EAAE,CAAC,MAAM,CAAC,qBAAqB,CAAC,CAAC,CAAM,mBAAmB;QAC1D,EAAE,CAAC,MAAM,CAAC,qBAAqB,CAAC,CAAC,CAAM,wBAAwB;QAC/D,EAAE,CAAC,MAAM,CAAC,uBAAuB,CAAC,CAAC,CAAI,2BAA2B;QAElE,4BAA4B;QAC5B,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,YAAY,CAAC,CAAC;QACtD,MAAM,MAAM,GAAG,EAAE,CAAC,YAAY,CAAC,UAAU,EAAE,OAAO,CAAC,CAAC;QACpD,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QAEhB,OAAO,IAAI,kBAAkB,CAAC,EAAE,EAAE,MAAM,CAAC,CAAC;IAC5C,CAAC;IAED;;OAEG;IACH,MAAM,CAAC,IAAI,CAAC,MAAc;QACxB,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,MAAM,CAAC,EAAE,CAAC;YAC3B,MAAM,IAAI,KAAK,CAAC,uBAAuB,MAAM,EAAE,CAAC,CAAC;QACnD,CAAC;QAED,MAAM,EAAE,GAAG,IAAI,wBAAQ,CAAC,MAAM,CAAC,CAAC;QAEhC,mCAAmC;QACnC,EAAE,CAAC,MAAM,CAAC,mBAAmB,CAAC,CAAC;QAC/B,EAAE,CAAC,MAAM,CAAC,oBAAoB,CAAC,CAAC;QAChC,qBAAqB;QACrB,EAAE,CAAC,MAAM,CAAC,sBAAsB,CAAC,CAAC;QAClC,EAAE,CAAC,MAAM,CAAC,qBAAqB,CAAC,CAAC;QACjC,EAAE,CAAC,MAAM,CAAC,qBAAqB,CAAC,CAAC;QACjC,EAAE,CAAC,MAAM,CAAC,uBAAuB,CAAC,CAAC;QAEnC,qCAAqC;QACrC,MAAM,IAAI,GAAG,IAAI,kBAAkB,CAAC,EAAE,EAAE,MAAM,CAAC,CAAC;QAChD,MAAM,cAAc,GAAG,IAAA,8BAAiB,EAAC,EAAE,CAAC,CAAC;QAE7C,IAAI,cAAc,GAAG,mCAAsB,EAAE,CAAC;YAC5C,IAAA,0BAAa,EAAC,EAAE,EAAE,cAAc,CAAC,CAAC;QACpC,CAAC;QAED,OAAO,IAAI,CAAC;IACd,CAAC;IAED;;OAEG;IACH,KAAK;QACH,OAAO,IAAI,CAAC,EAAE,CAAC;IACjB,CAAC;IAED;;OAEG;IACH,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC;IACrB,CAAC;IAED;;OAEG;IACH,gBAAgB;QACd,MAAM,GAAG,GAAG,IAAI,CAAC,EAAE;aAChB,OAAO,CAAC,4FAA4F,CAAC;aACrG,GAAG,EAAqF,CAAC;QAE5F,IAAI,CAAC,GAAG;YAAE,OAAO,IAAI,CAAC;QAEtB,OAAO;YACL,OAAO,EAAE,GAAG,CAAC,OAAO;YACpB,SAAS,EAAE,GAAG,CAAC,UAAU;YACzB,WAAW,EAAE,GAAG,CAAC,WAAW,IAAI,SAAS;SAC1C,CAAC;IACJ,CAAC;IAED;;OAEG;IACH,WAAW,CAAI,EAAW;QACxB,OAAO,IAAI,CAAC,EAAE,CAAC,WAAW,CAAC,EAAE,CAAC,EAAE,CAAC;IACnC,CAAC;IAED;;OAEG;IACH,OAAO;QACL,MAAM,KAAK,GAAG,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QACvC,OAAO,KAAK,CAAC,IAAI,CAAC;IACpB,CAAC;IAED;;OAEG;IACH,QAAQ;QACN,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;QACvB,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;IAC1B,CAAC;IAED;;OAEG;IACH,KAAK;QACH,IAAI,CAAC,EAAE,CAAC,KAAK,EAAE,CAAC;IAClB,CAAC;IAED;;OAEG;IACH,MAAM;QACJ,OAAO,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC;IACtB,CAAC;CACF;AAxID,gDAwIC;AAED;;GAEG;AACU,QAAA,iBAAiB,GAAG,cAAc,CAAC;AAEhD;;GAEG;AACH,SAAgB,eAAe,CAAC,WAAmB;IACjD,OAAO,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,YAAY,EAAE,yBAAiB,CAAC,CAAC;AACjE,CAAC"}

package/dist/db/migrations.d.ts

@@ -7,7 +7,7 @@ import Database from 'better-sqlite3';
 /**
  * Current schema version
  */
-export declare const CURRENT_SCHEMA_VERSION = 1;
+export declare const CURRENT_SCHEMA_VERSION = 2;
 /**
  * Migration definition
  */

package/dist/db/migrations.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"migrations.d.ts","sourceRoot":"","sources":["../../src/db/migrations.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,QAAQ,MAAM,gBAAgB,CAAC;AAEtC;;GAEG;AACH,eAAO,MAAM,sBAAsB,IAAI,CAAC;AAExC;;GAEG;AACH,UAAU,SAAS;IACjB,OAAO,EAAE,MAAM,CAAC;IAChB,WAAW,EAAE,MAAM,CAAC;IACpB,EAAE,EAAE,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,KAAK,IAAI,CAAC;CACrC;AAsBD;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,GAAG,MAAM,CAU/D;AAWD;;GAEG;AACH,wBAAgB,aAAa,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EAAE,WAAW,EAAE,MAAM,GAAG,IAAI,CAiB9E;AAED;;GAEG;AACH,wBAAgB,cAAc,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,GAAG,OAAO,CAG7D;AAED;;GAEG;AACH,wBAAgB,oBAAoB,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,GAAG,SAAS,EAAE,CAKvE;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CACjC,EAAE,EAAE,QAAQ,CAAC,QAAQ,GACpB,KAAK,CAAC;IAAE,OAAO,EAAE,MAAM,CAAC;IAAC,SAAS,EAAE,MAAM,CAAC;IAAC,WAAW,EAAE,MAAM,GAAG,IAAI,CAAA;CAAE,CAAC,CAU3E"}
+{"version":3,"file":"migrations.d.ts","sourceRoot":"","sources":["../../src/db/migrations.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,QAAQ,MAAM,gBAAgB,CAAC;AAEtC;;GAEG;AACH,eAAO,MAAM,sBAAsB,IAAI,CAAC;AAExC;;GAEG;AACH,UAAU,SAAS;IACjB,OAAO,EAAE,MAAM,CAAC;IAChB,WAAW,EAAE,MAAM,CAAC;IACpB,EAAE,EAAE,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,KAAK,IAAI,CAAC;CACrC;AAqBD;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,GAAG,MAAM,CAU/D;AAWD;;GAEG;AACH,wBAAgB,aAAa,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EAAE,WAAW,EAAE,MAAM,GAAG,IAAI,CAiB9E;AAED;;GAEG;AACH,wBAAgB,cAAc,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,GAAG,OAAO,CAG7D;AAED;;GAEG;AACH,wBAAgB,oBAAoB,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,GAAG,SAAS,EAAE,CAKvE;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CACjC,EAAE,EAAE,QAAQ,CAAC,QAAQ,GACpB,KAAK,CAAC;IAAE,OAAO,EAAE,MAAM,CAAC;IAAC,SAAS,EAAE,MAAM,CAAC;IAAC,WAAW,EAAE,MAAM,GAAG,IAAI,CAAA;CAAE,CAAC,CAU3E"}

package/dist/db/migrations.js

@@ -14,7 +14,7 @@ exports.getMigrationHistory = getMigrationHistory;
 /**
  * Current schema version
  */
-exports.CURRENT_SCHEMA_VERSION = 1;
+exports.CURRENT_SCHEMA_VERSION = 2;
 /**
  * All migrations in order
  *
@@ -22,17 +22,16 @@ exports.CURRENT_SCHEMA_VERSION = 1;
  * Future migrations go here.
  */
 const migrations = [
-// Example migration for version 2 (when needed):
-// {
-//   version: 2,
-//   description: 'Add support for module resolution',
-//   up: (db) => {
-//     db.exec(`
-//       ALTER TABLE nodes ADD COLUMN module_path TEXT;
-//       CREATE INDEX idx_nodes_module_path ON nodes(module_path);
-//     `);
-//   },
-// },
+    {
+        version: 2,
+        description: 'Add filePath and language to unresolved_refs for performance',
+        up: (db) => {
+            db.exec(`
+        ALTER TABLE unresolved_refs ADD COLUMN file_path TEXT;
+        ALTER TABLE unresolved_refs ADD COLUMN language TEXT;
+      `);
+        },
+    },
 ];
 /**
  * Get the current schema version from the database

package/dist/db/migrations.js.map

@@ -1 +1 @@
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package/dist/db/queries.d.ts

@@ -54,6 +54,10 @@ export declare class QueryBuilder {
      * Get all nodes of a specific kind
      */
     getNodesByKind(kind: NodeKind): Node[];
+    /**
+     * Get all nodes in the database
+     */
+    getAllNodes(): Node[];
     /**
      * Search nodes by name using FTS with fallback to LIKE for better matching
      *
@@ -116,6 +120,10 @@ export declare class QueryBuilder {
      * Insert an unresolved reference
      */
     insertUnresolvedRef(ref: UnresolvedReference): void;
+    /**
+     * Insert multiple unresolved references in a single transaction
+     */
+    insertUnresolvedRefsBatch(refs: UnresolvedReference[]): void;
     /**
      * Delete unresolved references from a node
      */

package/dist/db/queries.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"queries.d.ts","sourceRoot":"","sources":["../../src/db/queries.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,QAAQ,MAAM,gBAAgB,CAAC;AACtC,OAAO,EACL,IAAI,EACJ,IAAI,EACJ,UAAU,EACV,mBAAmB,EACnB,QAAQ,EACR,QAAQ,EAER,UAAU,EACV,aAAa,EACb,YAAY,EACb,MAAM,UAAU,CAAC;AAwHlB;;GAEG;AACH,qBAAa,YAAY;IACvB,OAAO,CAAC,EAAE,CAAoB;IAG9B,OAAO,CAAC,SAAS,CAAgC;IACjD,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAQ;IAGrC,OAAO,CAAC,KAAK,CAsBN;gBAEK,EAAE,EAAE,QAAQ,CAAC,QAAQ;IAQjC;;OAEG;IACH,UAAU,CAAC,IAAI,EAAE,IAAI,GAAG,IAAI;IA2C5B;;OAEG;IACH,WAAW,CAAC,KAAK,EAAE,IAAI,EAAE,GAAG,IAAI;IAQhC;;OAEG;IACH,UAAU,CAAC,IAAI,EAAE,IAAI,GAAG,IAAI;IAsD5B;;OAEG;IACH,UAAU,CAAC,EAAE,EAAE,MAAM,GAAG,IAAI;IAS5B;;OAEG;IACH,iBAAiB,CAAC,QAAQ,EAAE,MAAM,GAAG,IAAI;IAazC;;OAEG;IACH,WAAW,CAAC,EAAE,EAAE,MAAM,GAAG,IAAI,GAAG,IAAI;IAuBpC;;OAEG;IACH,OAAO,CAAC,SAAS;IAWjB;;OAEG;IACH,UAAU,IAAI,IAAI;IAIlB;;OAEG;IACH,cAAc,CAAC,QAAQ,EAAE,MAAM,GAAG,IAAI,EAAE;IAUxC;;OAEG;IACH,cAAc,CAAC,IAAI,EAAE,QAAQ,GAAG,IAAI,EAAE;IAQtC;;OAEG;IACH,WAAW,IAAI,IAAI,EAAE;IAKrB;;;;;;;OAOG;IACH,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,OAAO,GAAE,aAAkB,GAAG,YAAY,EAAE;IAcvE;;OAEG;IACH,OAAO,CAAC,cAAc;IAkDtB;;;OAGG;IACH,OAAO,CAAC,eAAe;IA4DvB;;OAEG;IACH,UAAU,CAAC,IAAI,EAAE,IAAI,GAAG,IAAI;IAkB5B;;OAEG;IACH,WAAW,CAAC,KAAK,EAAE,IAAI,EAAE,GAAG,IAAI;IAQhC;;OAEG;IACH,mBAAmB,CAAC,QAAQ,EAAE,MAAM,GAAG,IAAI;IAO3C;;OAEG;IACH,gBAAgB,CAAC,QAAQ,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE;IAc9D;;OAEG;IACH,gBAAgB,CAAC,QAAQ,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE;IAkB9D;;OAEG;IACH,UAAU,CAAC,IAAI,EAAE,UAAU,GAAG,IAAI;IA4BlC;;OAEG;IACH,UAAU,CAAC,QAAQ,EAAE,MAAM,GAAG,IAAI;IAUlC;;OAEG;IACH,aAAa,CAAC,QAAQ,EAAE,MAAM,GAAG,UAAU,GAAG,IAAI;IAQlD;;OAEG;IACH,WAAW,IAAI,UAAU,EAAE;IAQ3B;;OAEG;IACH,aAAa,CAAC,aAAa,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,UAAU,EAAE;IAY/D;;OAEG;IACH,mBAAmB,CAAC,GAAG,EAAE,mBAAmB,GAAG,IAAI;IAoBnD;;OAEG;IACH,yBAAyB,CAAC,IAAI,EAAE,mBAAmB,EAAE,GAAG,IAAI;IA0B5D;;OAEG;IACH,sBAAsB,CAAC,MAAM,EAAE,MAAM,GAAG,IAAI;IAS5C;;OAEG;IACH,mBAAmB,CAAC,IAAI,EAAE,MAAM,GAAG,mBAAmB,EAAE;IAmBxD;;OAEG;IACH,uBAAuB,IAAI,mBAAmB,EAAE;IAchD;;OAEG;IACH,yBAAyB,IAAI,IAAI;IAIjC;;OAEG;IACH,wBAAwB,CAAC,WAAW,EAAE,MAAM,EAAE,GAAG,IAAI;IAUrD;;OAEG;IACH,QAAQ,IAAI,UAAU;IAiDtB;;OAEG;IACH,KAAK,IAAI,IAAI;CAUd"}

package/dist/db/queries.js

@@ -6,6 +6,7 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.QueryBuilder = void 0;
+const utils_1 = require("../utils");
 /**
  * Convert database row to Node object
  */
@@ -28,8 +29,8 @@ function rowToNode(row) {
         isAsync: row.is_async === 1,
         isStatic: row.is_static === 1,
         isAbstract: row.is_abstract === 1,
-        decorators: row.decorators ? JSON.parse(row.decorators) : undefined,
-        typeParameters: row.type_parameters ? JSON.parse(row.type_parameters) : undefined,
+        decorators: row.decorators ? (0, utils_1.safeJsonParse)(row.decorators, undefined) : undefined,
+        typeParameters: row.type_parameters ? (0, utils_1.safeJsonParse)(row.type_parameters, undefined) : undefined,
         updatedAt: row.updated_at,
     };
 }
@@ -41,7 +42,7 @@ function rowToEdge(row) {
         source: row.source,
         target: row.target,
         kind: row.kind,
-        metadata: row.metadata ? JSON.parse(row.metadata) : undefined,
+        metadata: row.metadata ? (0, utils_1.safeJsonParse)(row.metadata, undefined) : undefined,
         line: row.line ?? undefined,
         column: row.col ?? undefined,
     };
@@ -58,7 +59,7 @@ function rowToFileRecord(row) {
         modifiedAt: row.modified_at,
         indexedAt: row.indexed_at,
         nodeCount: row.node_count,
-        errors: row.errors ? JSON.parse(row.errors) : undefined,
+        errors: row.errors ? (0, utils_1.safeJsonParse)(row.errors, undefined) : undefined,
     };
 }
 /**
@@ -83,7 +84,7 @@ class QueryBuilder {
     insertNode(node) {
         if (!this.stmts.insertNode) {
             this.stmts.insertNode = this.db.prepare(`
-        INSERT INTO nodes (
+        INSERT OR REPLACE INTO nodes (
           id, kind, name, qualified_name, file_path, language,
           start_line, end_line, start_column, end_column,
           docstring, signature, visibility,
@@ -273,6 +274,13 @@ class QueryBuilder {
         const rows = this.stmts.getNodesByKind.all(kind);
         return rows.map(rowToNode);
     }
+    /**
+     * Get all nodes in the database
+     */
+    getAllNodes() {
+        const rows = this.db.prepare('SELECT * FROM nodes').all();
+        return rows.map(rowToNode);
+    }
     /**
      * Search nodes by name using FTS with fallback to LIKE for better matching
      *
@@ -396,7 +404,7 @@ class QueryBuilder {
     insertEdge(edge) {
         if (!this.stmts.insertEdge) {
             this.stmts.insertEdge = this.db.prepare(`
-        INSERT INTO edges (source, target, kind, metadata, line, col)
+        INSERT OR IGNORE INTO edges (source, target, kind, metadata, line, col)
         VALUES (@source, @target, @kind, @metadata, @line, @col)
       `);
         }
@@ -541,8 +549,8 @@ class QueryBuilder {
     insertUnresolvedRef(ref) {
         if (!this.stmts.insertUnresolved) {
             this.stmts.insertUnresolved = this.db.prepare(`
-        INSERT INTO unresolved_refs (from_node_id, reference_name, reference_kind, line, col, candidates)
-        VALUES (@fromNodeId, @referenceName, @referenceKind, @line, @col, @candidates)
+        INSERT INTO unresolved_refs (from_node_id, reference_name, reference_kind, line, col, file_path, language, candidates)
+        VALUES (@fromNodeId, @referenceName, @referenceKind, @line, @col, @filePath, @language, @candidates)
       `);
         }
         this.stmts.insertUnresolved.run({
@@ -551,9 +559,38 @@ class QueryBuilder {
             referenceKind: ref.referenceKind,
             line: ref.line,
             col: ref.column,
+            filePath: ref.filePath ?? null,
+            language: ref.language ?? null,
             candidates: ref.candidates ? JSON.stringify(ref.candidates) : null,
         });
     }
+    /**
+     * Insert multiple unresolved references in a single transaction
+     */
+    insertUnresolvedRefsBatch(refs) {
+        if (refs.length === 0)
+            return;
+        if (!this.stmts.insertUnresolved) {
+            this.stmts.insertUnresolved = this.db.prepare(`
+        INSERT INTO unresolved_refs (from_node_id, reference_name, reference_kind, line, col, file_path, language, candidates)
+        VALUES (@fromNodeId, @referenceName, @referenceKind, @line, @col, @filePath, @language, @candidates)
+      `);
+        }
+        this.db.transaction(() => {
+            for (const ref of refs) {
+                this.stmts.insertUnresolved.run({
+                    fromNodeId: ref.fromNodeId,
+                    referenceName: ref.referenceName,
+                    referenceKind: ref.referenceKind,
+                    line: ref.line,
+                    col: ref.column,
+                    filePath: ref.filePath ?? null,
+                    language: ref.language ?? null,
+                    candidates: ref.candidates ? JSON.stringify(ref.candidates) : null,
+                });
+            }
+        })();
+    }
     /**
      * Delete unresolved references from a node
      */
@@ -577,7 +614,9 @@ class QueryBuilder {
             referenceKind: row.reference_kind,
             line: row.line,
             column: row.col,
-            candidates: row.candidates ? JSON.parse(row.candidates) : undefined,
+            filePath: row.file_path ?? undefined,
+            language: row.language ?? undefined,
+            candidates: row.candidates ? (0, utils_1.safeJsonParse)(row.candidates, []) : undefined,
         }));
     }
     /**
@@ -591,7 +630,9 @@ class QueryBuilder {
             referenceKind: row.reference_kind,
             line: row.line,
             column: row.col,
-            candidates: row.candidates ? JSON.parse(row.candidates) : undefined,
+            filePath: row.file_path ?? undefined,
+            language: row.language ?? undefined,
+            candidates: row.candidates ? (0, utils_1.safeJsonParse)(row.candidates, []) : undefined,
         }));
     }
     /**