seu-claude 1.0.1 → 1.0.2

package/CHANGELOG.md

@@ -5,6 +5,27 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.0.2] - 2026-01-16
+
+### Added
+
+- **Incremental Indexing** - New `FileIndex` class tracks file hashes and mtimes to skip unchanged files during re-indexing
+- **Progress Reporting** - Callback-based progress reporting during indexing with phase tracking (crawling, analyzing, embedding, saving)
+- CLI now shows real-time progress during `seu-claude index` command
+- `IndexResult` now includes `filesSkipped`, `filesUpdated`, and `filesDeleted` counts
+
+### Changed
+
+- `index_codebase` MCP tool output now shows incremental statistics
+- Improved indexing performance by only processing changed files
+- Better memory efficiency during large codebase indexing
+
+### Technical Details
+
+- **Test Coverage**: 301 tests passing
+- **New Classes**: `FileIndex` for persistent file tracking
+- **New Types**: `IndexProgress`, `IndexPhase`, `ProgressCallback`
+
 ## [1.0.1] - 2026-01-15
 
 ### Changed

package/dist/__tests__/file-index.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=file-index.test.d.ts.map

package/dist/__tests__/file-index.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"file-index.test.d.ts","sourceRoot":"","sources":["../../src/__tests__/file-index.test.ts"],"names":[],"mappings":""}

package/dist/__tests__/file-index.test.js

@@ -0,0 +1,252 @@
+import { describe, it, expect, beforeEach, afterEach } from '@jest/globals';
+import { FileIndex } from '../indexer/file-index.js';
+import { mkdir, rm, writeFile, readFile } from 'fs/promises';
+import { join } from 'path';
+import { tmpdir } from 'os';
+describe('FileIndex', () => {
+    let testDir;
+    let dataDir;
+    let fileIndex;
+    beforeEach(async () => {
+        testDir = join(tmpdir(), `seu-claude-file-index-test-${Date.now()}-${Math.random()}`);
+        dataDir = join(testDir, '.seu-claude');
+        await mkdir(dataDir, { recursive: true });
+        fileIndex = new FileIndex(dataDir, testDir);
+    });
+    afterEach(async () => {
+        await rm(testDir, { recursive: true, force: true });
+    });
+    describe('load', () => {
+        it('should handle missing index file gracefully', async () => {
+            await fileIndex.load();
+            expect(fileIndex.isLoaded()).toBe(true);
+            expect(fileIndex.size).toBe(0);
+        });
+        it('should load existing index file', async () => {
+            const indexPath = join(dataDir, 'file-index.json');
+            const data = {
+                version: 1,
+                projectRoot: testDir,
+                files: {
+                    'src/test.ts': {
+                        relativePath: 'src/test.ts',
+                        hash: 'abc123',
+                        mtime: 1234567890,
+                        indexedAt: 1234567890,
+                        chunkCount: 5,
+                    },
+                },
+            };
+            await writeFile(indexPath, JSON.stringify(data));
+            await fileIndex.load();
+            expect(fileIndex.isLoaded()).toBe(true);
+            expect(fileIndex.size).toBe(1);
+            expect(fileIndex.getFile('src/test.ts')).toEqual({
+                relativePath: 'src/test.ts',
+                hash: 'abc123',
+                mtime: 1234567890,
+                indexedAt: 1234567890,
+                chunkCount: 5,
+            });
+        });
+        it('should reset on version mismatch', async () => {
+            const indexPath = join(dataDir, 'file-index.json');
+            const data = {
+                version: 999, // Wrong version
+                projectRoot: testDir,
+                files: {
+                    'test.ts': {
+                        relativePath: 'test.ts',
+                        hash: 'abc',
+                        mtime: 0,
+                        indexedAt: 0,
+                        chunkCount: 1,
+                    },
+                },
+            };
+            await writeFile(indexPath, JSON.stringify(data));
+            await fileIndex.load();
+            expect(fileIndex.size).toBe(0); // Should be empty due to version mismatch
+        });
+        it('should reset on project root change', async () => {
+            const indexPath = join(dataDir, 'file-index.json');
+            const data = {
+                version: 1,
+                projectRoot: '/different/project', // Different project
+                files: {
+                    'test.ts': {
+                        relativePath: 'test.ts',
+                        hash: 'abc',
+                        mtime: 0,
+                        indexedAt: 0,
+                        chunkCount: 1,
+                    },
+                },
+            };
+            await writeFile(indexPath, JSON.stringify(data));
+            await fileIndex.load();
+            expect(fileIndex.size).toBe(0);
+        });
+        it('should handle corrupted JSON gracefully', async () => {
+            const indexPath = join(dataDir, 'file-index.json');
+            await writeFile(indexPath, 'not valid json {{{');
+            await fileIndex.load();
+            expect(fileIndex.isLoaded()).toBe(true);
+            expect(fileIndex.size).toBe(0);
+        });
+    });
+    describe('save', () => {
+        it('should save index to file', async () => {
+            await fileIndex.load();
+            fileIndex.updateFile('test.ts', {
+                hash: 'abc123',
+                mtime: 1234567890,
+                indexedAt: 1234567891,
+                chunkCount: 3,
+            });
+            await fileIndex.save();
+            const content = await readFile(join(dataDir, 'file-index.json'), 'utf-8');
+            const data = JSON.parse(content);
+            expect(data.version).toBe(1);
+            expect(data.projectRoot).toBe(testDir);
+            expect(data.files['test.ts']).toEqual({
+                relativePath: 'test.ts',
+                hash: 'abc123',
+                mtime: 1234567890,
+                indexedAt: 1234567891,
+                chunkCount: 3,
+            });
+        });
+        it('should create data directory if it does not exist', async () => {
+            await rm(dataDir, { recursive: true, force: true });
+            fileIndex = new FileIndex(dataDir, testDir);
+            await fileIndex.load();
+            fileIndex.updateFile('test.ts', { hash: 'abc', mtime: 0, indexedAt: 0, chunkCount: 1 });
+            await fileIndex.save();
+            const content = await readFile(join(dataDir, 'file-index.json'), 'utf-8');
+            expect(JSON.parse(content).files['test.ts']).toBeDefined();
+        });
+    });
+    describe('clear', () => {
+        it('should clear all files', async () => {
+            await fileIndex.load();
+            fileIndex.updateFile('test1.ts', { hash: 'abc', mtime: 0, indexedAt: 0, chunkCount: 1 });
+            fileIndex.updateFile('test2.ts', { hash: 'def', mtime: 0, indexedAt: 0, chunkCount: 2 });
+            await fileIndex.save();
+            await fileIndex.clear();
+            expect(fileIndex.size).toBe(0);
+        });
+    });
+    describe('getChangedFiles', () => {
+        it('should detect new files', async () => {
+            await fileIndex.load();
+            const currentFiles = [createFileInfo('new-file.ts', 'hash1', Date.now())];
+            const changed = fileIndex.getChangedFiles(currentFiles);
+            expect(changed).toHaveLength(1);
+            expect(changed[0].relativePath).toBe('new-file.ts');
+        });
+        it('should detect files with changed hash', async () => {
+            await fileIndex.load();
+            fileIndex.updateFile('existing.ts', {
+                hash: 'old-hash',
+                mtime: 1000,
+                indexedAt: 1000,
+                chunkCount: 5,
+            });
+            const currentFiles = [createFileInfo('existing.ts', 'new-hash', 1000)];
+            const changed = fileIndex.getChangedFiles(currentFiles);
+            expect(changed).toHaveLength(1);
+            expect(changed[0].relativePath).toBe('existing.ts');
+        });
+        it('should detect files with changed mtime', async () => {
+            await fileIndex.load();
+            fileIndex.updateFile('existing.ts', {
+                hash: 'same-hash',
+                mtime: 1000,
+                indexedAt: 1000,
+                chunkCount: 5,
+            });
+            const currentFiles = [
+                createFileInfo('existing.ts', 'same-hash', 2000), // Different mtime
+            ];
+            const changed = fileIndex.getChangedFiles(currentFiles);
+            expect(changed).toHaveLength(1);
+        });
+        it('should not include unchanged files', async () => {
+            await fileIndex.load();
+            fileIndex.updateFile('unchanged.ts', {
+                hash: 'same-hash',
+                mtime: 1000,
+                indexedAt: 1000,
+                chunkCount: 5,
+            });
+            const currentFiles = [
+                createFileInfo('unchanged.ts', 'same-hash', 1000),
+                createFileInfo('new.ts', 'new-hash', 2000),
+            ];
+            const changed = fileIndex.getChangedFiles(currentFiles);
+            expect(changed).toHaveLength(1);
+            expect(changed[0].relativePath).toBe('new.ts');
+        });
+    });
+    describe('getDeletedFiles', () => {
+        it('should detect deleted files', async () => {
+            await fileIndex.load();
+            fileIndex.updateFile('deleted.ts', { hash: 'abc', mtime: 0, indexedAt: 0, chunkCount: 1 });
+            fileIndex.updateFile('still-exists.ts', {
+                hash: 'def',
+                mtime: 0,
+                indexedAt: 0,
+                chunkCount: 2,
+            });
+            const currentFiles = [createFileInfo('still-exists.ts', 'def', 0)];
+            const deleted = fileIndex.getDeletedFiles(currentFiles);
+            expect(deleted).toHaveLength(1);
+            expect(deleted[0]).toBe('deleted.ts');
+        });
+        it('should return empty array when no files deleted', async () => {
+            await fileIndex.load();
+            fileIndex.updateFile('file1.ts', { hash: 'abc', mtime: 0, indexedAt: 0, chunkCount: 1 });
+            const currentFiles = [createFileInfo('file1.ts', 'abc', 0)];
+            const deleted = fileIndex.getDeletedFiles(currentFiles);
+            expect(deleted).toHaveLength(0);
+        });
+    });
+    describe('updateFile and removeFile', () => {
+        it('should update file record', async () => {
+            await fileIndex.load();
+            fileIndex.updateFile('test.ts', {
+                hash: 'abc123',
+                mtime: 1000,
+                indexedAt: 2000,
+                chunkCount: 10,
+            });
+            const record = fileIndex.getFile('test.ts');
+            expect(record).toEqual({
+                relativePath: 'test.ts',
+                hash: 'abc123',
+                mtime: 1000,
+                indexedAt: 2000,
+                chunkCount: 10,
+            });
+        });
+        it('should remove file record', async () => {
+            await fileIndex.load();
+            fileIndex.updateFile('test.ts', { hash: 'abc', mtime: 0, indexedAt: 0, chunkCount: 1 });
+            fileIndex.removeFile('test.ts');
+            expect(fileIndex.getFile('test.ts')).toBeUndefined();
+            expect(fileIndex.size).toBe(0);
+        });
+    });
+});
+function createFileInfo(relativePath, hash, mtime) {
+    return {
+        path: `/test/${relativePath}`,
+        relativePath,
+        language: 'typescript',
+        hash,
+        size: 100,
+        modifiedAt: new Date(mtime),
+    };
+}
+//# sourceMappingURL=file-index.test.js.map

package/dist/__tests__/file-index.test.js.map

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package/dist/__tests__/tools.test.js

@@ -76,12 +76,18 @@ describe('IndexResult interface', () => {
             chunksCreated: 50,
             languages: { typescript: 5, python: 3, rust: 2 },
             durationMs: 1500,
+            filesSkipped: 5,
+            filesUpdated: 10,
+            filesDeleted: 2,
         };
         expect(result.success).toBe(true);
         expect(result.filesProcessed).toBe(10);
         expect(result.chunksCreated).toBe(50);
         expect(result.languages).toEqual({ typescript: 5, python: 3, rust: 2 });
         expect(result.durationMs).toBe(1500);
+        expect(result.filesSkipped).toBe(5);
+        expect(result.filesUpdated).toBe(10);
+        expect(result.filesDeleted).toBe(2);
         expect(result.error).toBeUndefined();
     });
     it('should have correct structure for failure', () => {
@@ -91,9 +97,13 @@ describe('IndexResult interface', () => {
             chunksCreated: 0,
             languages: {},
             durationMs: 100,
+            filesSkipped: 0,
+            filesUpdated: 0,
+            filesDeleted: 0,
             error: 'Something went wrong',
         };
         expect(result.success).toBe(false);
+        expect(result.filesSkipped).toBe(0);
         expect(result.error).toBe('Something went wrong');
     });
 });

package/dist/__tests__/tools.test.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"cli-index.d.ts","sourceRoot":"","sources":["../src/cli-index.ts"],"names":[],"mappings":";AAEA;;;GAGG;AAOH,wBAAsB,QAAQ,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CA0E9D"}
+{"version":3,"file":"cli-index.d.ts","sourceRoot":"","sources":["../src/cli-index.ts"],"names":[],"mappings":";AAEA;;;GAGG;AAQH,wBAAsB,QAAQ,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAwG9D"}

package/dist/cli-index.js

@@ -36,13 +36,44 @@ export async function runIndex(pathArg) {
         await embedder.initialize();
         await store.initialize();
         console.log('✅ Components ready\n');
+        // Progress callback for CLI
+        let lastPhase = '';
+        const onProgress = (progress) => {
+            // Only log phase changes to avoid too much output
+            if (progress.phase !== lastPhase) {
+                const phaseEmoji = {
+                    crawling: '🔍',
+                    analyzing: '📝',
+                    embedding: '🧠',
+                    saving: '💾',
+                    complete: '✅',
+                };
+                console.log(`${phaseEmoji[progress.phase] || '📦'} ${progress.message}`);
+                lastPhase = progress.phase;
+            }
+            else if (progress.current && progress.total && progress.current % 10 === 0) {
+                // Log every 10 files during analysis
+                process.stdout.write(`\r   ${progress.current}/${progress.total} files processed`);
+            }
+        };
         // Run indexing
-        console.log('� Indexing codebase...');
+        console.log('📦 Indexing codebase...');
         const startTime = Date.now();
-        const result = await indexTool.execute(false);
+        const result = await indexTool.execute(false, onProgress);
+        console.log(''); // Clear progress line
         const duration = ((Date.now() - startTime) / 1000).toFixed(2);
         if (result.success) {
             console.log(`\n✅ Indexed ${result.filesProcessed} files with ${result.chunksCreated} chunks (${duration}s)`);
+            if (result.filesSkipped > 0 || result.filesDeleted > 0) {
+                const stats = [];
+                if (result.filesSkipped > 0)
+                    stats.push(`${result.filesSkipped} unchanged`);
+                if (result.filesUpdated > 0)
+                    stats.push(`${result.filesUpdated} updated`);
+                if (result.filesDeleted > 0)
+                    stats.push(`${result.filesDeleted} deleted`);
+                console.log(`   (${stats.join(', ')})`);
+            }
             console.log('\n📊 Languages:');
             for (const [lang, count] of Object.entries(result.languages)) {
                 console.log(`   ${lang}: ${count} files`);

package/dist/cli-index.js.map

@@ -1 +1 @@
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package/dist/indexer/file-index.d.ts

@@ -0,0 +1,28 @@
+import type { FileInfo } from './crawler.js';
+export interface IndexedFileInfo {
+    relativePath: string;
+    hash: string;
+    mtime: number;
+    indexedAt: number;
+    chunkCount: number;
+}
+export declare class FileIndex {
+    private dataDir;
+    private projectRoot;
+    private files;
+    private log;
+    private loaded;
+    constructor(dataDir: string, projectRoot: string);
+    private get filePath();
+    load(): Promise<void>;
+    save(): Promise<void>;
+    clear(): Promise<void>;
+    getChangedFiles(currentFiles: FileInfo[]): FileInfo[];
+    getDeletedFiles(currentFiles: FileInfo[]): string[];
+    updateFile(relativePath: string, info: Omit<IndexedFileInfo, 'relativePath'>): void;
+    removeFile(relativePath: string): void;
+    getFile(relativePath: string): IndexedFileInfo | undefined;
+    get size(): number;
+    isLoaded(): boolean;
+}
+//# sourceMappingURL=file-index.d.ts.map

package/dist/indexer/file-index.d.ts.map

@@ -0,0 +1 @@
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package/dist/indexer/file-index.js

@@ -0,0 +1,117 @@
+import { readFile, writeFile, mkdir } from 'fs/promises';
+import { join, dirname } from 'path';
+import { logger } from '../utils/logger.js';
+const FILE_INDEX_VERSION = 1;
+const FILE_INDEX_NAME = 'file-index.json';
+export class FileIndex {
+    dataDir;
+    projectRoot;
+    files = new Map();
+    log = logger.child('file-index');
+    loaded = false;
+    constructor(dataDir, projectRoot) {
+        this.dataDir = dataDir;
+        this.projectRoot = projectRoot;
+    }
+    get filePath() {
+        return join(this.dataDir, FILE_INDEX_NAME);
+    }
+    async load() {
+        try {
+            const content = await readFile(this.filePath, 'utf-8');
+            const data = JSON.parse(content);
+            if (data.version !== FILE_INDEX_VERSION) {
+                this.log.warn(`File index version mismatch (expected ${FILE_INDEX_VERSION}, got ${data.version}). Starting fresh.`);
+                this.files = new Map();
+                this.loaded = true;
+                return;
+            }
+            if (data.projectRoot !== this.projectRoot) {
+                this.log.warn('Project root changed. Starting fresh.');
+                this.files = new Map();
+                this.loaded = true;
+                return;
+            }
+            this.files = new Map(Object.entries(data.files));
+            this.log.info(`Loaded file index with ${this.files.size} files`);
+            this.loaded = true;
+        }
+        catch (err) {
+            if (err.code === 'ENOENT') {
+                this.log.info('No existing file index found, starting fresh');
+            }
+            else {
+                this.log.warn('Failed to load file index, starting fresh:', err);
+            }
+            this.files = new Map();
+            this.loaded = true;
+        }
+    }
+    async save() {
+        const data = {
+            version: FILE_INDEX_VERSION,
+            projectRoot: this.projectRoot,
+            files: Object.fromEntries(this.files),
+        };
+        await mkdir(dirname(this.filePath), { recursive: true });
+        await writeFile(this.filePath, JSON.stringify(data, null, 2));
+        this.log.debug(`Saved file index with ${this.files.size} files`);
+    }
+    async clear() {
+        this.files = new Map();
+        try {
+            const { unlink } = await import('fs/promises');
+            await unlink(this.filePath);
+        }
+        catch {
+            // File doesn't exist, that's fine
+        }
+        this.log.info('Cleared file index');
+    }
+    getChangedFiles(currentFiles) {
+        const changed = [];
+        for (const file of currentFiles) {
+            const indexed = this.files.get(file.relativePath);
+            if (!indexed) {
+                // New file
+                changed.push(file);
+                continue;
+            }
+            // Check if mtime or hash changed
+            const currentMtime = file.modifiedAt.getTime();
+            if (indexed.mtime !== currentMtime || indexed.hash !== file.hash) {
+                changed.push(file);
+            }
+        }
+        return changed;
+    }
+    getDeletedFiles(currentFiles) {
+        const currentPaths = new Set(currentFiles.map(f => f.relativePath));
+        const deleted = [];
+        for (const [relativePath] of this.files) {
+            if (!currentPaths.has(relativePath)) {
+                deleted.push(relativePath);
+            }
+        }
+        return deleted;
+    }
+    updateFile(relativePath, info) {
+        this.files.set(relativePath, {
+            relativePath,
+            ...info,
+        });
+    }
+    removeFile(relativePath) {
+        this.files.delete(relativePath);
+    }
+    getFile(relativePath) {
+        return this.files.get(relativePath);
+    }
+    get size() {
+        return this.files.size;
+    }
+    isLoaded() {
+        return this.loaded;
+    }
+}
+//# sourceMappingURL=file-index.js.map

package/dist/indexer/file-index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"file-index.js","sourceRoot":"","sources":["../../src/indexer/file-index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,KAAK,EAAE,MAAM,aAAa,CAAC;AACzD,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,MAAM,CAAC;AACrC,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAC;AAG5C,MAAM,kBAAkB,GAAG,CAAC,CAAC;AAC7B,MAAM,eAAe,GAAG,iBAAiB,CAAC;AAgB1C,MAAM,OAAO,SAAS;IACZ,OAAO,CAAS;IAChB,WAAW,CAAS;IACpB,KAAK,GAAiC,IAAI,GAAG,EAAE,CAAC;IAChD,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC;IACjC,MAAM,GAAG,KAAK,CAAC;IAEvB,YAAY,OAAe,EAAE,WAAmB;QAC9C,IAAI,CAAC,OAAO,GAAG,OAAO,CAAC;QACvB,IAAI,CAAC,WAAW,GAAG,WAAW,CAAC;IACjC,CAAC;IAED,IAAY,QAAQ;QAClB,OAAO,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE,eAAe,CAAC,CAAC;IAC7C,CAAC;IAED,KAAK,CAAC,IAAI;QACR,IAAI,CAAC;YACH,MAAM,OAAO,GAAG,MAAM,QAAQ,CAAC,IAAI,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;YACvD,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAkB,CAAC;YAElD,IAAI,IAAI,CAAC,OAAO,KAAK,kBAAkB,EAAE,CAAC;gBACxC,IAAI,CAAC,GAAG,CAAC,IAAI,CACX,yCAAyC,kBAAkB,SAAS,IAAI,CAAC,OAAO,oBAAoB,CACrG,CAAC;gBACF,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,EAAE,CAAC;gBACvB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC;gBACnB,OAAO;YACT,CAAC;YAED,IAAI,IAAI,CAAC,WAAW,KAAK,IAAI,CAAC,WAAW,EAAE,CAAC;gBAC1C,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,uCAAuC,CAAC,CAAC;gBACvD,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,EAAE,CAAC;gBACvB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC;gBACnB,OAAO;YACT,CAAC;YAED,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC;YACjD,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,0BAA0B,IAAI,CAAC,KAAK,CAAC,IAAI,QAAQ,CAAC,CAAC;YACjE,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC;QACrB,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,IAAK,GAA6B,CAAC,IAAI,KAAK,QAAQ,EAAE,CAAC;gBACrD,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,8CAA8C,CAAC,CAAC;YAChE,CAAC;iBAAM,CAAC;gBACN,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,4CAA4C,EAAE,GAAG,CAAC,CAAC;YACnE,CAAC;YACD,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,EAAE,CAAC;YACvB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC;QACrB,CAAC;IACH,CAAC;IAED,KAAK,CAAC,IAAI;QACR,MAAM,IAAI,GAAkB;YAC1B,OAAO,EAAE,kBAAkB;YAC3B,WAAW,EAAE,IAAI,CAAC,WAAW;YAC7B,KAAK,EAAE,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC;SACtC,CAAC;QAEF,MAAM,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QACzD,MAAM,SAAS,CAAC,IAAI,CAAC,QAAQ,EAAE,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QAC9D,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,yBAAyB,IAAI,CAAC,KAAK,CAAC,IAAI,QAAQ,CAAC,CAAC;IACnE,CAAC;IAED,KAAK,CAAC,KAAK;QACT,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,EAAE,CAAC;QACvB,IAAI,CAAC;YACH,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,CAAC;YAC/C,MAAM,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;QAC9B,CAAC;QAAC,MAAM,CAAC;YACP,kCAAkC;QACpC,CAAC;QACD,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC;IACtC,CAAC;IAED,eAAe,CAAC,YAAwB;QACtC,MAAM,OAAO,GAAe,EAAE,CAAC;QAE/B,KAAK,MAAM,IAAI,IAAI,YAAY,EAAE,CAAC;YAChC,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;YAElD,IAAI,CAAC,OAAO,EAAE,CAAC;gBACb,WAAW;gBACX,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;gBACnB,SAAS;YACX,CAAC;YAED,iCAAiC;YACjC,MAAM,YAAY,GAAG,IAAI,CAAC,UAAU,CAAC,OAAO,EAAE,CAAC;YAC/C,IAAI,OAAO,CAAC,KAAK,KAAK,YAAY,IAAI,OAAO,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,EAAE,CAAC;gBACjE,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;YACrB,CAAC;QACH,CAAC;QAED,OAAO,OAAO,CAAC;IACjB,CAAC;IAED,eAAe,CAAC,YAAwB;QACtC,MAAM,YAAY,GAAG,IAAI,GAAG,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC;QACpE,MAAM,OAAO,GAAa,EAAE,CAAC;QAE7B,KAAK,MAAM,CAAC,YAAY,CAAC,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC;YACxC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,CAAC;gBACpC,OAAO,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;YAC7B,CAAC;QACH,CAAC;QAED,OAAO,OAAO,CAAC;IACjB,CAAC;IAED,UAAU,CAAC,YAAoB,EAAE,IAA2C;QAC1E,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,YAAY,EAAE;YAC3B,YAAY;YACZ,GAAG,IAAI;SACR,CAAC,CAAC;IACL,CAAC;IAED,UAAU,CAAC,YAAoB;QAC7B,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,YAAY,CAAC,CAAC;IAClC,CAAC;IAED,OAAO,CAAC,YAAoB;QAC1B,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC;IACtC,CAAC;IAED,IAAI,IAAI;QACN,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC;IACzB,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC;IACrB,CAAC;CACF"}

package/dist/server.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"server.d.ts","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":"AAOA,OAAO,EAAE,MAAM,EAAc,MAAM,mBAAmB,CAAC;AASvD,qBAAa,eAAe;IAC1B,OAAO,CAAC,MAAM,CAAS;IACvB,OAAO,CAAC,MAAM,CAAS;IACvB,OAAO,CAAC,QAAQ,CAAkB;IAClC,OAAO,CAAC,KAAK,CAAc;IAC3B,OAAO,CAAC,SAAS,CAAgB;IACjC,OAAO,CAAC,UAAU,CAAiB;IACnC,OAAO,CAAC,WAAW,CAAsB;IACzC,OAAO,CAAC,SAAS,CAAc;IAC/B,OAAO,CAAC,GAAG,CAA0B;IACrC,OAAO,CAAC,WAAW,CAAS;gBAEhB,MAAM,CAAC,EAAE,OAAO,CAAC,MAAM,CAAC;IAwBpC,OAAO,CAAC,aAAa;IA2CrB,OAAO,CAAC,kBAAkB;YAiHZ,iBAAiB;YAajB,mBAAmB;YAyBnB,oBAAoB;YAqBpB,iBAAiB;YAsBjB,iBAAiB;IAoBzB,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAMtB,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;CAK5B"}
+{"version":3,"file":"server.d.ts","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":"AAOA,OAAO,EAAE,MAAM,EAAc,MAAM,mBAAmB,CAAC;AASvD,qBAAa,eAAe;IAC1B,OAAO,CAAC,MAAM,CAAS;IACvB,OAAO,CAAC,MAAM,CAAS;IACvB,OAAO,CAAC,QAAQ,CAAkB;IAClC,OAAO,CAAC,KAAK,CAAc;IAC3B,OAAO,CAAC,SAAS,CAAgB;IACjC,OAAO,CAAC,UAAU,CAAiB;IACnC,OAAO,CAAC,WAAW,CAAsB;IACzC,OAAO,CAAC,SAAS,CAAc;IAC/B,OAAO,CAAC,GAAG,CAA0B;IACrC,OAAO,CAAC,WAAW,CAAS;gBAEhB,MAAM,CAAC,EAAE,OAAO,CAAC,MAAM,CAAC;IAwBpC,OAAO,CAAC,aAAa;IA2CrB,OAAO,CAAC,kBAAkB;YAiHZ,iBAAiB;YAajB,mBAAmB;YA4CnB,oBAAoB;YAqBpB,iBAAiB;YAsBjB,iBAAiB;IAoBzB,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAMtB,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;CAK5B"}

package/dist/server.js

@@ -196,11 +196,31 @@ export class SeuClaudeServer {
             this.config.projectRoot = path;
         }
         const result = await this.indexTool.execute(force);
-        const text = result.success
-            ? `Successfully indexed ${result.filesProcessed} files with ${result.chunksCreated} code chunks in ${(result.durationMs / 1000).toFixed(1)}s.\n\nLanguages: ${Object.entries(result.languages)
-                .map(([lang, count]) => `${lang}: ${count}`)
-                .join(', ')}`
-            : `Indexing failed: ${result.error}`;
+        let text;
+        if (result.success) {
+            const parts = [
+                `Successfully indexed ${result.filesProcessed} files with ${result.chunksCreated} code chunks in ${(result.durationMs / 1000).toFixed(1)}s.`,
+            ];
+            if (result.filesSkipped > 0 || result.filesDeleted > 0) {
+                const stats = [];
+                if (result.filesSkipped > 0)
+                    stats.push(`${result.filesSkipped} unchanged`);
+                if (result.filesUpdated > 0)
+                    stats.push(`${result.filesUpdated} updated`);
+                if (result.filesDeleted > 0)
+                    stats.push(`${result.filesDeleted} deleted`);
+                parts.push(`\n(${stats.join(', ')})`);
+            }
+            if (Object.keys(result.languages).length > 0) {
+                parts.push(`\n\nLanguages: ${Object.entries(result.languages)
+                    .map(([lang, count]) => `${lang}: ${count}`)
+                    .join(', ')}`);
+            }
+            text = parts.join('');
+        }
+        else {
+            text = `Indexing failed: ${result.error}`;
+        }
         return {
             content: [{ type: 'text', text }],
         };

package/dist/server.js.map

@@ -1 +1 @@
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+{"version":3,"file":"server.js","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,2CAA2C,CAAC;AACnE,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EACL,qBAAqB,EACrB,sBAAsB,GAEvB,MAAM,oCAAoC,CAAC;AAC5C,OAAO,EAAU,UAAU,EAAE,MAAM,mBAAmB,CAAC;AACvD,OAAO,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAC3C,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AACpD,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAChD,OAAO,EAAE,aAAa,EAAE,MAAM,2BAA2B,CAAC;AAC1D,OAAO,EAAE,cAAc,EAAE,MAAM,4BAA4B,CAAC;AAC5D,OAAO,EAAE,mBAAmB,EAAE,MAAM,yBAAyB,CAAC;AAC9D,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAEtD,MAAM,OAAO,eAAe;IAClB,MAAM,CAAS;IACf,MAAM,CAAS;IACf,QAAQ,CAAkB;IAC1B,KAAK,CAAc;IACnB,SAAS,CAAgB;IACzB,UAAU,CAAiB;IAC3B,WAAW,CAAsB;IACjC,SAAS,CAAc;IACvB,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC;IAC7B,WAAW,GAAG,KAAK,CAAC;IAE5B,YAAY,MAAwB;QAClC,IAAI,CAAC,MAAM,GAAG,UAAU,CAAC,MAAM,CAAC,CAAC;QACjC,IAAI,CAAC,QAAQ,GAAG,IAAI,eAAe,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QACjD,IAAI,CAAC,KAAK,GAAG,IAAI,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QAC1C,IAAI,CAAC,SAAS,GAAG,IAAI,aAAa,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,QAAQ,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC;QAC3E,IAAI,CAAC,UAAU,GAAG,IAAI,cAAc,CAAC,IAAI,CAAC,QAAQ,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC;QAChE,IAAI,CAAC,WAAW,GAAG,IAAI,mBAAmB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACvD,IAAI,CAAC,SAAS,GAAG,IAAI,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QAE9C,IAAI,CAAC,MAAM,GAAG,IAAI,MAAM,CACtB;YACE,IAAI,EAAE,YAAY;YAClB,OAAO,EAAE,OAAO;SACjB,EACD;YACE,YAAY,EAAE;gBACZ,KAAK,EAAE,EAAE;aACV;SACF,CACF,CAAC;QAEF,IAAI,CAAC,aAAa,EAAE,CAAC;IACvB,CAAC;IAEO,aAAa;QACnB,uBAAuB;QACvB,IAAI,CAAC,MAAM,CAAC,iBAAiB,CAAC,sBAAsB,EAAE,GAAG,EAAE;YACzD,OAAO;gBACL,KAAK,EAAE,IAAI,CAAC,kBAAkB,EAAE;aACjC,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,oBAAoB;QACpB,IAAI,CAAC,MAAM,CAAC,iBAAiB,CAAC,qBAAqB,EAAE,KAAK,EAAC,OAAO,EAAC,EAAE;YACnE,MAAM,EAAE,IAAI,EAAE,SAAS,EAAE,IAAI,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC;YAEjD,IAAI,CAAC;gBACH,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAC;gBAE/B,QAAQ,IAAI,EAAE,CAAC;oBACb,KAAK,gBAAgB;wBACnB,OAAO,MAAM,IAAI,CAAC,mBAAmB,CAAC,IAAI,CAAC,CAAC;oBAC9C,KAAK,iBAAiB;wBACpB,OAAO,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,CAAC;oBAC/C,KAAK,uBAAuB;wBAC1B,OAAO,MAAM,IAAI,CAAC,iBAAiB,CAAC,IAAI,CAAC,CAAC;oBAC5C,KAAK,cAAc;wBACjB,OAAO,MAAM,IAAI,CAAC,iBAAiB,CAAC,IAAI,CAAC,CAAC;oBAC5C;wBACE,MAAM,IAAI,KAAK,CAAC,iBAAiB,IAAI,EAAE,CAAC,CAAC;gBAC7C,CAAC;YACH,CAAC;YAAC,OAAO,GAAG,EAAE,CAAC;gBACb,MAAM,KAAK,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC/D,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,QAAQ,IAAI,UAAU,EAAE,KAAK,CAAC,CAAC;gBAC9C,OAAO;oBACL,OAAO,EAAE;wBACP;4BACE,IAAI,EAAE,MAAM;4BACZ,IAAI,EAAE,UAAU,KAAK,EAAE;yBACxB;qBACF;oBACD,OAAO,EAAE,IAAI;iBACd,CAAC;YACJ,CAAC;QACH,CAAC,CAAC,CAAC;IACL,CAAC;IAEO,kBAAkB;QACxB,OAAO;YACL;gBACE,IAAI,EAAE,gBAAgB;gBACtB,WAAW,EACT,uPAAuP;gBACzP,WAAW,EAAE;oBACX,IAAI,EAAE,QAAQ;oBACd,UAAU,EAAE;wBACV,IAAI,EAAE;4BACJ,IAAI,EAAE,QAAQ;4BACd,WAAW,EACT,2FAA2F;yBAC9F;wBACD,KAAK,EAAE;4BACL,IAAI,EAAE,SAAS;4BACf,WAAW,EACT,sFAAsF;yBACzF;qBACF;iBACF;aACF;YACD;gBACE,IAAI,EAAE,iBAAiB;gBACvB,WAAW,EACT,2PAA2P;gBAC7P,WAAW,EAAE;oBACX,IAAI,EAAE,QAAQ;oBACd,UAAU,EAAE;wBACV,KAAK,EAAE;4BACL,IAAI,EAAE,QAAQ;4BACd,WAAW,EACT,oIAAoI;yBACvI;wBACD,KAAK,EAAE;4BACL,IAAI,EAAE,QAAQ;4BACd,WAAW,EAAE,mDAAmD;yBACjE;wBACD,WAAW,EAAE;4BACX,IAAI,EAAE,QAAQ;4BACd,IAAI,EAAE,CAAC,UAAU,EAAE,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,CAAC;4BAC5E,WAAW,EAAE,wCAAwC;yBACtD;wBACD,eAAe,EAAE;4BACf,IAAI,EAAE,QAAQ;4BACd,WAAW,EACT,gFAAgF;yBACnF;qBACF;oBACD,QAAQ,EAAE,CAAC,OAAO,CAAC;iBACpB;aACF;YACD;gBACE,IAAI,EAAE,uBAAuB;gBAC7B,WAAW,EACT,qNAAqN;gBACvN,WAAW,EAAE;oBACX,IAAI,EAAE,QAAQ;oBACd,UAAU,EAAE;wBACV,SAAS,EAAE;4BACT,IAAI,EAAE,QAAQ;4BACd,WAAW,EAAE,4BAA4B;yBAC1C;wBACD,MAAM,EAAE;4BACN,IAAI,EAAE,QAAQ;4BACd,WAAW,EACT,sHAAsH;yBACzH;wBACD,UAAU,EAAE;4BACV,IAAI,EAAE,QAAQ;4BACd,WAAW,EAAE,6CAA6C;yBAC3D;wBACD,QAAQ,EAAE;4BACR,IAAI,EAAE,QAAQ;4BACd,WAAW,EAAE,2CAA2C;yBACzD;wBACD,aAAa,EAAE;4BACb,IAAI,EAAE,QAAQ;4BACd,WAAW,EAAE,qEAAqE;yBACnF;qBACF;oBACD,QAAQ,EAAE,CAAC,WAAW,CAAC;iBACxB;aACF;YACD;gBACE,IAAI,EAAE,cAAc;gBACpB,WAAW,EACT,4LAA4L;gBAC9L,WAAW,EAAE;oBACX,IAAI,EAAE,QAAQ;oBACd,UAAU,EAAE;wBACV,MAAM,EAAE;4BACN,IAAI,EAAE,QAAQ;4BACd,WAAW,EACT,yFAAyF;yBAC5F;wBACD,SAAS,EAAE;4BACT,IAAI,EAAE,QAAQ;4BACd,IAAI,EAAE,CAAC,SAAS,EAAE,SAAS,EAAE,MAAM,CAAC;4BACpC,WAAW,EACT,0GAA0G;yBAC7G;wBACD,WAAW,EAAE;4BACX,IAAI,EAAE,QAAQ;4BACd,WAAW,EAAE,mDAAmD;yBACjE;qBACF;oBACD,QAAQ,EAAE,CAAC,QAAQ,CAAC;iBACrB;aACF;SACF,CAAC;IACJ,CAAC;IAEO,KAAK,CAAC,iBAAiB;QAC7B,IAAI,IAAI,CAAC,WAAW;YAAE,OAAO;QAE7B,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,mCAAmC,CAAC,CAAC;QAEnD,MAAM,IAAI,CAAC,KAAK,CAAC,UAAU,EAAE,CAAC;QAC9B,MAAM,IAAI,CAAC,QAAQ,CAAC,UAAU,EAAE,CAAC;QACjC,MAAM,IAAI,CAAC,SAAS,CAAC,UAAU,EAAE,CAAC;QAElC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC;QACxB,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,iCAAiC,CAAC,CAAC;IACnD,CAAC;IAEO,KAAK,CAAC,mBAAmB,CAC/B,IAAyC;QAEzC,MAAM,IAAI,GAAG,IAAI,EAAE,IAA0B,CAAC;QAC9C,MAAM,KAAK,GAAG,IAAI,EAAE,KAA4B,CAAC;QAEjD,IAAI,IAAI,EAAE,CAAC;YACT,IAAI,CAAC,MAAM,CAAC,WAAW,GAAG,IAAI,CAAC;QACjC,CAAC;QAED,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,OAAO,CAA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package/dist/tools/index-codebase.d.ts

@@ -7,8 +7,23 @@ export interface IndexResult {
     chunksCreated: number;
     languages: Record<string, number>;
     durationMs: number;
+    filesSkipped: number;
+    filesUpdated: number;
+    filesDeleted: number;
     error?: string;
 }
+export type IndexPhase = 'crawling' | 'analyzing' | 'embedding' | 'saving' | 'complete';
+export interface IndexProgress {
+    phase: IndexPhase;
+    message: string;
+    /** Current item being processed (e.g., file number) */
+    current?: number;
+    /** Total items to process */
+    total?: number;
+    /** Current file path being processed */
+    currentFile?: string;
+}
+export type ProgressCallback = (progress: IndexProgress) => void;
 export declare class IndexCodebase {
     private config;
     private crawler;
@@ -19,7 +34,7 @@ export declare class IndexCodebase {
     private initialized;
     constructor(config: Config, embedder: EmbeddingEngine, store: VectorStore, languagesDir?: string);
     initialize(): Promise<void>;
-    execute(force?: boolean): Promise<IndexResult>;
+    execute(force?: boolean, onProgress?: ProgressCallback): Promise<IndexResult>;
     private embedAndStore;
     private saveXrefGraph;
 }

package/dist/tools/index-codebase.d.ts.map

@@ -1 +1 @@
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package/dist/tools/index-codebase.js

@@ -1,5 +1,6 @@
 import { Crawler } from '../indexer/crawler.js';
 import { SemanticChunker } from '../indexer/chunker.js';
+import { FileIndex } from '../indexer/file-index.js';
 import { logger } from '../utils/logger.js';
 import { readFile, writeFile, mkdir } from 'fs/promises';
 import { join, dirname } from 'path';
@@ -24,27 +25,100 @@ export class IndexCodebase {
         await this.chunker.initialize();
         this.initialized = true;
     }
-    async execute(force = false) {
+    async execute(force = false, onProgress) {
         const startTime = Date.now();
+        const report = (progress) => {
+            if (onProgress)
+                onProgress(progress);
+        };
         try {
             await this.initialize();
             this.log.info(`Starting indexing of ${this.config.projectRoot}${force ? ' (force)' : ''}`);
+            report({ phase: 'crawling', message: 'Scanning files...' });
+            // Initialize file index for incremental tracking
+            const fileIndex = new FileIndex(this.config.dataDir, this.config.projectRoot);
             if (force) {
                 await this.store.clear();
+                await fileIndex.clear();
+            }
+            else {
+                await fileIndex.load();
             }
             // Crawl the codebase
             const crawlResult = await this.crawler.crawl();
             this.log.info(`Found ${crawlResult.totalFiles} files (${(crawlResult.totalSize / 1024 / 1024).toFixed(2)} MB)`);
+            report({
+                phase: 'crawling',
+                message: `Found ${crawlResult.totalFiles} files`,
+                total: crawlResult.totalFiles,
+            });
+            // Handle deleted files
+            const deletedFiles = fileIndex.getDeletedFiles(crawlResult.files);
+            for (const relativePath of deletedFiles) {
+                const indexed = fileIndex.getFile(relativePath);
+                if (indexed) {
+                    // Convert relative path to absolute for deletion
+                    const absolutePath = join(this.config.projectRoot, relativePath);
+                    await this.store.deleteByFilePath(absolutePath);
+                    fileIndex.removeFile(relativePath);
+                    this.log.debug(`Removed deleted file: ${relativePath}`);
+                }
+            }
+            // Get changed/new files
+            const changedFiles = fileIndex.getChangedFiles(crawlResult.files);
+            const skippedCount = crawlResult.totalFiles - changedFiles.length;
+            if (changedFiles.length === 0 && deletedFiles.length === 0) {
+                this.log.info('No changes detected, index is up to date');
+                return {
+                    success: true,
+                    filesProcessed: 0,
+                    chunksCreated: 0,
+                    languages: crawlResult.languages,
+                    durationMs: Date.now() - startTime,
+                    filesSkipped: skippedCount,
+                    filesUpdated: 0,
+                    filesDeleted: 0,
+                };
+            }
+            this.log.info(`Processing ${changedFiles.length} changed files (${skippedCount} unchanged, ${deletedFiles.length} deleted)`);
+            report({
+                phase: 'analyzing',
+                message: `Processing ${changedFiles.length} files`,
+                current: 0,
+                total: changedFiles.length,
+            });
             let chunksCreated = 0;
-            const batchSize = 50; // Process files in batches for memory efficiency
+            const batchSize = 50;
             const allChunks = [];
-            // Process files and create chunks
-            for (const file of crawlResult.files) {
+            const fileChunkCounts = new Map();
+            let processedCount = 0;
+            // Process changed files
+            for (const file of changedFiles) {
+                processedCount++;
+                report({
+                    phase: 'analyzing',
+                    message: `Analyzing ${file.relativePath}`,
+                    current: processedCount,
+                    total: changedFiles.length,
+                    currentFile: file.relativePath,
+                });
                 try {
+                    // Delete old chunks for this file if it was previously indexed
+                    const existingRecord = fileIndex.getFile(file.relativePath);
+                    if (existingRecord) {
+                        await this.store.deleteByFilePath(file.path);
+                    }
                     const content = await readFile(file.path, 'utf-8');
                     const chunks = await this.chunker.chunkFile(file.path, file.relativePath, content, file.language);
+                    // Track chunk count for this file
+                    fileChunkCounts.set(file.relativePath, chunks.length);
                     allChunks.push(...chunks);
                     if (allChunks.length >= batchSize) {
+                        report({
+                            phase: 'embedding',
+                            message: `Generating embeddings (${chunksCreated + allChunks.length} chunks)`,
+                            current: chunksCreated + allChunks.length,
+                        });
                         await this.embedAndStore(allChunks);
                         chunksCreated += allChunks.length;
                         allChunks.length = 0;
@@ -56,20 +130,50 @@ export class IndexCodebase {
             }
             // Process remaining chunks
             if (allChunks.length > 0) {
+                report({
+                    phase: 'embedding',
+                    message: `Generating final embeddings (${chunksCreated + allChunks.length} total chunks)`,
+                    current: chunksCreated + allChunks.length,
+                });
                 await this.embedAndStore(allChunks);
                 chunksCreated += allChunks.length;
             }
+            report({
+                phase: 'saving',
+                message: 'Saving index...',
+            });
+            // Update file index with processed files
+            for (const file of changedFiles) {
+                const chunkCount = fileChunkCounts.get(file.relativePath) ?? 0;
+                fileIndex.updateFile(file.relativePath, {
+                    hash: file.hash,
+                    mtime: file.modifiedAt.getTime(),
+                    indexedAt: Date.now(),
+                    chunkCount,
+                });
+            }
+            // Save file index
+            await fileIndex.save();
             // Finalize cross-references and save the graph
             this.chunker.finalizeXrefs();
             await this.saveXrefGraph();
             const durationMs = Date.now() - startTime;
-            this.log.info(`Indexing complete: ${chunksCreated} chunks from ${crawlResult.totalFiles} files in ${(durationMs / 1000).toFixed(1)}s`);
+            this.log.info(`Indexing complete: ${chunksCreated} chunks from ${changedFiles.length} files in ${(durationMs / 1000).toFixed(1)}s`);
+            report({
+                phase: 'complete',
+                message: `Indexed ${chunksCreated} chunks from ${changedFiles.length} files`,
+                current: changedFiles.length,
+                total: changedFiles.length,
+            });
             return {
                 success: true,
-                filesProcessed: crawlResult.totalFiles,
+                filesProcessed: changedFiles.length,
                 chunksCreated,
                 languages: crawlResult.languages,
                 durationMs,
+                filesSkipped: skippedCount,
+                filesUpdated: changedFiles.length,
+                filesDeleted: deletedFiles.length,
             };
         }
         catch (err) {
@@ -81,6 +185,9 @@ export class IndexCodebase {
                 chunksCreated: 0,
                 languages: {},
                 durationMs: Date.now() - startTime,
+                filesSkipped: 0,
+                filesUpdated: 0,
+                filesDeleted: 0,
                 error,
             };
         }

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "seu-claude",
-  "version": "1.0.1",
+  "version": "1.0.2",
   "description": "Local Codebase RAG MCP Server for Claude Code - Proactive semantic indexing with AST-based chunking",
   "type": "module",
   "main": "dist/index.js",