@veewo/gitnexus 1.5.6 → 1.5.7

package/dist/cli/analyze.js

@@ -18,11 +18,10 @@ import { getCurrentCommit, isGitRepo, getGitRoot } from '../storage/git.js';
 import { generateAIContextFiles } from './ai-context.js';
 import { generateSkillFiles } from './skill-gen.js';
 import fs from 'fs/promises';
-import { resolveEffectiveAnalyzeOptions } from './analyze-options.js';
+import { resolveEffectiveAnalyzeOptions, validateStoredOptions } from './analyze-options.js';
 import { formatCSharpPreprocDiagnosticsSummary, formatFallbackSummary, formatUnityDiagnosticsSummary, formatUnityRuleBindingSummary, resolveFallbackStats, } from './analyze-summary.js';
 import { resolveChildProcessExit } from './exit-code.js';
 import { toPipelineRuntimeSummary } from './analyze-runtime-summary.js';
-import { enforceSyncManifestConsistency, resolveScopeManifestForAnalyze } from './sync-manifest.js';
 const HEAP_MB = 8192;
 const HEAP_FLAG = `--max-old-space-size=${HEAP_MB}`;
 /** Re-exec the process with an 8GB heap if we're currently below that. */
@@ -111,31 +110,22 @@ export const analyzeCommand = async (inputPath, options) => {
     let scopeRules = [];
     let repoAlias;
     let embeddingsEnabled = false;
+    let csharpDefineCsproj;
     try {
-        const scopeManifest = await resolveScopeManifestForAnalyze(repoPath, {
-            scopeManifest: options?.scopeManifest,
-            scopePrefix: options?.scopePrefix,
-        });
-        await enforceSyncManifestConsistency({
-            manifestPath: scopeManifest,
-            extensions: options?.extensions,
-            repoAlias: options?.repoAlias,
-            embeddings: options?.embeddings,
-            policy: options?.syncManifestPolicy,
-            stdinIsTTY: Boolean(process.stdin.isTTY),
-        });
+        const validatedStored = await validateStoredOptions(options?.reuseOptions !== false ? existingMeta?.analyzeOptions : undefined, repoPath);
         const effectiveOptions = await resolveEffectiveAnalyzeOptions({
             extensions: options?.extensions,
-            scopeManifest,
-            scopePrefix: options?.scopePrefix,
+            scope: options?.scope,
             repoAlias: options?.repoAlias,
             embeddings: options?.embeddings,
             reuseOptions: options?.reuseOptions,
-        }, existingMeta?.analyzeOptions);
+            csharpDefineCsproj: options?.csharpDefineCsproj,
+        }, validatedStored);
         includeExtensions = effectiveOptions.includeExtensions;
         scopeRules = effectiveOptions.scopeRules;
         repoAlias = effectiveOptions.repoAlias;
         embeddingsEnabled = effectiveOptions.embeddings;
+        csharpDefineCsproj = effectiveOptions.csharpDefineCsproj;
     }
     catch (error) {
         console.log(`  ${error?.message || String(error)}\n`);
@@ -146,13 +136,10 @@ export const analyzeCommand = async (inputPath, options) => {
         console.log('  Existing metadata found, but LadybugDB index file is missing — rebuilding index...\n');
     }
     if (existingMeta && hasLbugIndex && !options?.force && existingMeta.lastCommit === currentCommit && !options?.skills) {
-        const hasScopePrefixInput = Array.isArray(options?.scopePrefix)
-            ? options.scopePrefix.length > 0
-            : Boolean(options?.scopePrefix);
         const hasCliOverrides = options?.extensions !== undefined ||
-            Boolean(options?.scopeManifest) ||
-            hasScopePrefixInput ||
+            options?.scope !== undefined ||
             options?.repoAlias !== undefined ||
+            options?.csharpDefineCsproj !== undefined ||
             options?.embeddings !== undefined ||
             options?.reuseOptions === false;
         if (!hasCliOverrides) {
@@ -253,7 +240,7 @@ export const analyzeCommand = async (inputPath, options) => {
     // ── Phase 1: Full Pipeline (0–60%) ─────────────────────────────────
     let pipelineResult;
     try {
-        const pipelineRunOptions = buildPipelineRunOptionsForAnalyze({ includeExtensions, scopeRules }, options);
+        const pipelineRunOptions = buildPipelineRunOptionsForAnalyze({ includeExtensions, scopeRules, csharpDefineCsproj });
         pipelineResult = await runPipelineFromRepo(repoPath, (progress) => {
             const phaseLabel = PHASE_LABELS[progress.phase] || progress.phase;
             const scaled = Math.round(progress.percent * 0.6);
@@ -363,6 +350,7 @@ export const analyzeCommand = async (inputPath, options) => {
             scopeRules,
             repoAlias,
             embeddings: embeddingsEnabled,
+            ...(csharpDefineCsproj ? { csharpDefineCsproj } : {}),
         },
         stats: {
             files: pipelineRuntime.totalFileCount,
@@ -484,8 +472,8 @@ export function buildPipelineRunOptionsForAnalyze(resolvedOptions, options) {
     return {
         includeExtensions: resolvedOptions.includeExtensions,
         scopeRules: resolvedOptions.scopeRules,
-        ...(options?.csharpDefineCsproj
-            ? { csharpDefineCsproj: options.csharpDefineCsproj }
+        ...(resolvedOptions.csharpDefineCsproj
+            ? { csharpDefineCsproj: resolvedOptions.csharpDefineCsproj }
             : {}),
     };
 }

package/dist/cli/analyze.test.js

@@ -1,25 +1,19 @@
 import test from 'node:test';
 import assert from 'node:assert/strict';
-import path from 'node:path';
 import { buildPipelineRunOptionsForAnalyze } from './analyze.js';
-import { resolveScopeManifestForAnalyze } from './sync-manifest.js';
-test('analyze auto-loads .gitnexus/sync-manifest.txt when CLI scope options are omitted', async () => {
-    const repoPath = path.join('/tmp', 'demo-repo');
-    const expectedManifest = path.join(repoPath, '.gitnexus', 'sync-manifest.txt');
-    const resolved = await resolveScopeManifestForAnalyze(repoPath, {}, async (candidate) => candidate === expectedManifest);
-    assert.equal(resolved, expectedManifest);
-});
-test('explicit --scope-manifest still wins over auto-detected default file', async () => {
-    const repoPath = path.join('/tmp', 'demo-repo');
-    const explicitManifest = path.join(repoPath, 'custom-manifest.txt');
-    const resolved = await resolveScopeManifestForAnalyze(repoPath, { scopeManifest: explicitManifest }, async () => true);
-    assert.equal(resolved, explicitManifest);
-});
 test('buildPipelineRunOptionsForAnalyze passes csharp define csproj option through to pipeline', () => {
-    const out = buildPipelineRunOptionsForAnalyze({ includeExtensions: ['.cs'], scopeRules: ['Assets/**'] }, { csharpDefineCsproj: '/tmp/Assembly-CSharp.csproj' });
+    const out = buildPipelineRunOptionsForAnalyze({ includeExtensions: ['.cs'], scopeRules: ['Assets/**'], csharpDefineCsproj: '/tmp/Assembly-CSharp.csproj' });
     assert.deepEqual(out, {
         includeExtensions: ['.cs'],
         scopeRules: ['Assets/**'],
         csharpDefineCsproj: '/tmp/Assembly-CSharp.csproj',
     });
 });
+test('buildPipelineRunOptionsForAnalyze omits csharpDefineCsproj when not provided', () => {
+    const out = buildPipelineRunOptionsForAnalyze({ includeExtensions: ['.cs'], scopeRules: ['Assets/**'] });
+    assert.deepEqual(out, {
+        includeExtensions: ['.cs'],
+        scopeRules: ['Assets/**'],
+    });
+    assert.equal(Object.keys(out).includes('csharpDefineCsproj'), false);
+});

package/dist/cli/benchmark-agent-context.d.ts

@@ -17,8 +17,6 @@ export declare function benchmarkAgentContextCommand(dataset: string, options: {
     targetPath?: string;
     reportDir?: string;
     extensions?: string;
-    scopeManifest?: string;
-    scopePrefix?: string[];
     skipAnalyze?: boolean;
 }, deps?: {
     loadDataset?: (root: string) => Promise<AgentContextDataset>;

package/dist/cli/benchmark-agent-context.js

@@ -29,8 +29,6 @@ export async function benchmarkAgentContextCommand(dataset, options, deps) {
         const analyzeOptions = {
             extensions: options.extensions,
             repoAlias: options.repoAlias,
-            scopeManifest: options.scopeManifest,
-            scopePrefix: options.scopePrefix,
         };
         try {
             await analyze(analyzePath, analyzeOptions);

package/dist/cli/benchmark-agent-safe-query-context.d.ts

@@ -8,8 +8,6 @@ export declare function benchmarkAgentSafeQueryContextCommand(dataset: string, o
     reportDir?: string;
     subagentRunsDir?: string;
     extensions?: string;
-    scopeManifest?: string;
-    scopePrefix?: string[];
     skipAnalyze?: boolean;
 }, deps?: {
     loadSuite?: (root: string) => Promise<AgentSafeBenchmarkSuite>;

package/dist/cli/benchmark-agent-safe-query-context.js

@@ -16,8 +16,6 @@ export async function benchmarkAgentSafeQueryContextCommand(dataset, options, de
         await analyze(path.resolve(options.targetPath), {
             extensions: options.extensions,
             repoAlias: options.repoAlias,
-            scopeManifest: options.scopeManifest,
-            scopePrefix: options.scopePrefix,
         });
     }
     const suite = await loadSuite(path.resolve(dataset));

package/dist/cli/benchmark-unity.d.ts

@@ -9,7 +9,5 @@ export declare function benchmarkUnityCommand(dataset: string, options: {
     targetPath?: string;
     reportDir?: string;
     extensions?: string;
-    scopeManifest?: string;
-    scopePrefix?: string[];
     skipAnalyze?: boolean;
 }): Promise<void>;

package/dist/cli/benchmark-unity.js

@@ -19,8 +19,6 @@ export async function benchmarkUnityCommand(dataset, options) {
         profile: profileConfig,
         reportDir: options.reportDir,
         extensions: options.extensions,
-        scopeManifest: options.scopeManifest,
-        scopePrefix: options.scopePrefix,
         skipAnalyze: options.skipAnalyze ?? false,
     });
     process.stderr.write(`${result.pass ? 'PASS' : 'FAIL'}\n`);

package/dist/cli/clean.d.ts

@@ -1,9 +1,8 @@
 /**
  * Clean Command
  *
- * Removes the GitNexus index from the current repository while preserving
- * configuration files (e.g. sync-manifest.txt). Also unregisters the repo
- * from the global registry.
+ * Removes the GitNexus index from the current repository.
+ * Also unregisters the repo from the global registry.
  */
 export declare const cleanCommand: (options?: {
     force?: boolean;

package/dist/cli/clean.js

@@ -1,32 +1,11 @@
 /**
  * Clean Command
  *
- * Removes the GitNexus index from the current repository while preserving
- * configuration files (e.g. sync-manifest.txt). Also unregisters the repo
- * from the global registry.
+ * Removes the GitNexus index from the current repository.
+ * Also unregisters the repo from the global registry.
  */
 import fs from 'fs/promises';
-import path from 'path';
 import { findRepo, unregisterRepo, listRegisteredRepos } from '../storage/repo-manager.js';
-/** Files under .gitnexus/ that are configuration, not index data. */
-const PRESERVE_FILES = new Set(['sync-manifest.txt']);
-async function cleanStoragePath(storagePath) {
-    let entries;
-    try {
-        entries = await fs.readdir(storagePath);
-    }
-    catch (err) {
-        if (err.code === 'ENOENT')
-            return;
-        throw err;
-    }
-    for (const entry of entries) {
-        if (PRESERVE_FILES.has(entry))
-            continue;
-        const fullPath = path.join(storagePath, entry);
-        await fs.rm(fullPath, { recursive: true, force: true });
-    }
-}
 export const cleanCommand = async (options) => {
     // --all flag: clean all indexed repos
     if (options?.all) {
@@ -46,7 +25,7 @@ export const cleanCommand = async (options) => {
         const entries = await listRegisteredRepos();
         for (const entry of entries) {
             try {
-                await cleanStoragePath(entry.storagePath);
+                await fs.rm(entry.storagePath, { recursive: true, force: true });
                 await unregisterRepo(entry.path);
                 console.log(`Cleaned: ${entry.name} (${entry.storagePath})`);
             }
@@ -71,7 +50,7 @@ export const cleanCommand = async (options) => {
         return;
     }
     try {
-        await cleanStoragePath(repo.storagePath);
+        await fs.rm(repo.storagePath, { recursive: true, force: true });
         await unregisterRepo(repo.repoPath);
         console.log(`Cleaned: ${repo.storagePath}`);
     }

package/dist/cli/index.js

@@ -8,7 +8,6 @@ import { attachRuleLabCommands } from './rule-lab.js';
 const _require = createRequire(import.meta.url);
 const pkg = _require('../../package.json');
 const program = new Command();
-const collectValues = (value, previous) => [...previous, value];
 program
     .name('gitnexus')
     .description('GitNexus local CLI and MCP server')
@@ -29,12 +28,10 @@ program
     .option('--embeddings', 'Enable embedding generation for semantic search (off by default)')
     .option('--extensions <list>', 'Comma-separated file extensions to include (e.g. .cs,.ts)')
     .option('--repo-alias <name>', 'Override indexed repository name with a stable alias')
+    .option('--scope <rules>', 'Comma-separated scope path-prefix rules (e.g. Assets/,Packages/com.veewo.*)')
     .option('--csharp-define-csproj <path>', 'Load C# DefineConstants from the specified .csproj and normalize conditional-compilation blocks before parsing')
-    .option('--sync-manifest-policy <policy>', 'When CLI options differ from sync manifest directives: ask|update|keep|error (default: ask)')
     .option('--skills', 'Generate repo-specific skill files from detected communities')
     .option('-v, --verbose', 'Enable verbose ingestion warnings (default: false)')
-    .option('--scope-manifest <path>', 'Manifest file with scope rules (supports comments and * wildcard; recommended: .gitnexus/sync-manifest.txt)')
-    .option('--scope-prefix <pathPrefix>', 'Add a scope path prefix rule (repeatable)', collectValues, [])
     .addHelpText('after', '\nEnvironment variables:\n  GITNEXUS_NO_GITIGNORE=1  Skip .gitignore parsing (still reads .gitnexusignore)')
     .action(createLazyAction(() => import('./analyze.js'), 'analyzeCommand'));
 program
@@ -155,8 +152,6 @@ program
     .option('--target-path <path>', 'Path to analyze before evaluation (required unless --skip-analyze)')
     .option('--report-dir <path>', 'Output directory for benchmark-report.json and benchmark-summary.md', '.gitnexus/benchmark')
     .option('--extensions <list>', 'Analyze extension filter (comma-separated, optional)')
-    .option('--scope-manifest <path>', 'Analyze scope manifest file')
-    .option('--scope-prefix <pathPrefix>', 'Analyze scope path prefix (repeatable)', collectValues, [])
     .option('--skip-analyze', 'Skip analyze stage and evaluate current index only')
     .action(createLazyAction(() => import('./benchmark-unity.js'), 'benchmarkUnityCommand'));
 program
@@ -168,8 +163,6 @@ program
     .option('--target-path <path>', 'Path to analyze before evaluation (required unless --skip-analyze)')
     .option('--report-dir <path>', 'Output directory for benchmark-report.json and benchmark-summary.md', '.gitnexus/benchmark-agent-context')
     .option('--extensions <list>', 'Analyze extension filter (comma-separated, optional)')
-    .option('--scope-manifest <path>', 'Analyze scope manifest file')
-    .option('--scope-prefix <pathPrefix>', 'Analyze scope path prefix (repeatable)', collectValues, [])
     .option('--skip-analyze', 'Skip analyze stage and evaluate current index only')
     .action(createLazyAction(() => import('./benchmark-agent-context.js'), 'benchmarkAgentContextCommand'));
 program
@@ -181,8 +174,6 @@ program
     .option('--subagent-runs-dir <path>', 'Directory containing session-generated subagent run artifacts')
     .option('--report-dir <path>', 'Output directory for benchmark-report.json and benchmark-summary.md', '.gitnexus/benchmark-agent-safe-query-context')
     .option('--extensions <list>', 'Analyze extension filter (comma-separated, optional)')
-    .option('--scope-manifest <path>', 'Analyze scope manifest file')
-    .option('--scope-prefix <pathPrefix>', 'Analyze scope path prefix (repeatable)', collectValues, [])
     .option('--skip-analyze', 'Skip analyze stage and evaluate current index only')
     .action(createLazyAction(() => import('./benchmark-agent-safe-query-context.js'), 'benchmarkAgentSafeQueryContextCommand'));
 program

package/dist/core/ingestion/pipeline.js

@@ -79,7 +79,7 @@ export const runPipelineFromRepo = async (repoPath, onProgress, options) => {
         const scopeSelection = selectEntriesByScopeRules(scannedFiles, options?.scopeRules || []);
         const scopedFiles = scopeSelection.selected;
         if (scopeSelection.diagnostics.appliedRuleCount > 0 && scopedFiles.length === 0) {
-            throw new Error('Scope filters matched zero files. Check --scope-manifest/--scope-prefix.');
+            throw new Error('Scope filters matched zero files. Check your scope rules and extensions.');
         }
         const includeExtensions = new Set((options?.includeExtensions || [])
             .map(ext => ext.trim().toLowerCase())

package/dist/storage/repo-manager.d.ts

@@ -15,6 +15,7 @@ export interface RepoMeta {
         scopeRules?: string[];
         repoAlias?: string;
         embeddings?: boolean;
+        csharpDefineCsproj?: string;
     };
     stats?: {
         files?: number;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@veewo/gitnexus",
-  "version": "1.5.6",
+  "version": "1.5.7",
   "description": "Graph-powered code intelligence for AI agents. Index any codebase, query via MCP or CLI.",
   "author": "Abhigyan Patwari",
   "license": "PolyForm-Noncommercial-1.0.0",

package/skills/gitnexus-cli.md

@@ -60,73 +60,97 @@ $GN analyze
 
 Run from the project root. This parses all source files, builds the knowledge graph, writes it to `.gitnexus/`, and generates CLAUDE.md / AGENTS.md context files.
 
+Analyze options are resolved with two-layer priority: **CLI arguments** > **stored options** in `meta.json.analyzeOptions`. On first run, pass CLI flags; they are persisted automatically for subsequent runs.
+
 | Flag | Effect |
 |------|--------|
 | `--force` | Force full re-index even if up to date |
+| `--no-reuse-options` | Do not reuse stored analyze options from previous index |
 | `--embeddings` | Enable embedding generation (off by default) |
+| `--extensions <list>` | Comma-separated file extensions (e.g. `.cs,.ts`) |
+| `--scope <rules>` | Comma-separated scope path-prefix rules (e.g. `Assets/,Packages/com.veewo.*`) |
+| `--repo-alias <name>` | Override indexed repository name with a stable alias |
+| `--csharp-define-csproj <path>` | Load C# `DefineConstants` from `.csproj` for `#if` normalization |
 | `--skills` | Generate repo-specific skill files from detected communities |
+| `-v, --verbose` | Enable verbose ingestion warnings |
 
-**Two mutually exclusive paths. Choose one per rebuild.**
+**Option persistence:** `--extensions`, `--scope`, `--repo-alias`, `--embeddings`, and `--csharp-define-csproj` are automatically saved to `meta.json.analyzeOptions` after a successful run. On subsequent runs, these stored values are reused unless you pass new CLI flags or use `--no-reuse-options`.
 
-#### Path A: sync-manifest managed (recommended for Unity / monorepo)
+#### Scope rules
 
-If `.gitnexus/sync-manifest.txt` exists, `analyze` **auto-uses** it when you do **not** pass `--scope-prefix` or `--scope-manifest`.
+Scope rules control which files are included in the index. When no scope rules are stored, **all files** in the repo are indexed. Use `--scope` on first run to set scope rules; they are persisted automatically.
+
+**Scope rule semantics:**
+- Each rule is a **path prefix** — `Assets/` matches all files under `Assets/`
+- Trailing `*` is a **wildcard prefix** — `Packages/com.veewo.*` matches `Packages/com.veewo.stat/...`
+- No glob support: `Assets/**/*.cs` will not work
+- Empty scope = full repo scan (all files)
 
 ```bash
-# Unity project with an existing manifest — this is the normal rebuild command
+# Scope to specific directories
+$GN analyze --force --scope "Assets/,Packages/"
+
+# Wildcard scope
+$GN analyze --force --scope "Assets/NEON/Code,Packages/com.veewo.*"
+
+# No --scope = full repo (or reuse stored scope rules)
 $GN analyze --force
 ```
 
-The manifest controls scope rules, extensions, and repo alias. Example:
+#### Unity project recommended parameters
 
-```
-Assets/
-Packages/
-@extensions=.cs,.meta
-@repoAlias=neonspark-core
+Unity projects benefit from a specific combination of parameters to ensure correct C# parsing and optimal scope:
+
+```bash
+# Unity project — first-time index (recommended)
+$GN analyze --force \
+  --extensions ".cs,.meta" \
+  --scope "Assets/,Packages/" \
+  --repo-alias <repo-alias> \
+  --csharp-define-csproj <path-to-Assembly-CSharp.csproj>
+
+# Subsequent rebuilds (all options are reused automatically)
+$GN analyze --force
 ```
 
-- Non-`@` lines = path-prefix scope rules
-- `@extensions=<csv>` = file extension filter
-- `@repoAlias=<name>` = stable repo alias
-- `@embeddings=<true|false>` = embedding toggle
+| Parameter | Recommended value | Why |
+|-----------|------------------|-----|
+| `--extensions` | `.cs,.meta` | C# scripts + Unity `.meta` asset files for resource binding |
+| `--scope` | `Assets/,Packages/` | Limit to Unity project directories; skip `Library/`, `Temp/`, `obj/` |
+| `--csharp-define-csproj` | `path/to/Assembly-CSharp.csproj` | Normalize `#if` / `#elif` conditional compilation using project's `DefineConstants` |
+| `--repo-alias` | e.g. `neonspark-core` | Stable alias for MCP repo lookup regardless of directory name |
 
-**Drift guard:** If you pass `--extensions` / `--repo-alias` / `--embeddings` while a manifest exists, CLI compares them. Use `--sync-manifest-policy` to control: `ask|update|keep|error` (default `ask`; non-TTY requires explicit policy).
+**C# preprocessing detail:** Unity projects commonly use conditional compilation (`#if UNITY_EDITOR`, `#if NEON_DEBUG`, etc.). Without `--csharp-define-csproj`, tree-sitter parses each `#if` branch as-is, often producing incorrect AST for the active branch. The csproj path is persisted and reused automatically after first specification.
 
-**Do not mix Path A and Path B.** Passing `--scope-prefix` or `--extensions` when a manifest exists triggers the drift guard and may error out in non-TTY environments.
+**Scope for large Unity repos:** For repos where only specific packages matter, narrow scope instead of indexing all of `Assets/`:
 
-#### Path B: manual CLI flags (first-time or simple projects)
+```bash
+$GN analyze --force \
+  --scope "Assets/NEON/Code,Packages/com.veewo.*" \
+  --extensions ".cs,.meta" \
+  --repo-alias neonspark-core
+```
 
-Use when no sync-manifest exists:
+#### Other project examples
 
 ```bash
-# Unity project, first-time index
-$GN analyze --force --extensions ".cs,.meta" --scope-prefix Assets/ --repo-alias neonspark-core
+# Generic TypeScript project
+$GN analyze --force --extensions ".ts,.tsx" --repo-alias my-project
 
-# Generic project
-$GN analyze --force --extensions ".ts,.tsx" --scope-prefix src/
+# Subsequent rebuilds (stored options are reused automatically)
+$GN analyze --force
 ```
 
-| Manual flag | Effect |
-|-------------|--------|
-| `--extensions <ext>` | Comma-separated file extensions |
-| `--scope-prefix <prefix>` | Add a path prefix rule (repeatable) |
-| `--scope-manifest <file>` | Read scope rules from a manifest file |
-| `--repo-alias <name>` | Override indexed repository name |
-| `--csharp-define-csproj <path>` | Load C# `DefineConstants` from `.csproj` for `#if` normalization |
-
-**C# preprocessing (Unity):** For projects with heavy conditional compilation, add `--csharp-define-csproj /path/to/Assembly-CSharp.csproj` (neonspark: `/Volumes/Shuttle/projects/neonspark/Assembly-CSharp.csproj`). Without it, C# files are parsed raw and tree-sitter may mishandle `#if` branches.
-
 #### Rebuild recovery — when analyze hangs or crashes
 
 If `analyze --force` hangs (no progress after 5+ minutes) or crashes leaving a corrupted index:
 
 ```bash
-# 1. Clean the corrupted index (preserves sync-manifest.txt)
+# 1. Clean the corrupted index
 $GN clean --force
 
-# 2. Rebuild
-$GN analyze --force
+# 2. Rebuild (re-specify CLI options since meta.json was deleted)
+$GN analyze --force --extensions ".cs,.meta" --repo-alias neonspark-core
 ```
 
 **When to clean before rebuild:**
@@ -145,13 +169,13 @@ $GN status
 
 Shows whether the current repo has a GitNexus index, when it was last updated, and symbol/relationship counts. Use this to check if re-indexing is needed.
 
-### clean — Delete the index (preserves config)
+### clean — Delete the index
 
 ```bash
 $GN clean --force
 ```
 
-Removes the GitNexus index (graph, CSVs, LadybugDB) from `.gitnexus/` while **preserving `sync-manifest.txt`** and other configuration files. Use this to recover from a corrupted index before re-indexing.
+Removes the entire `.gitnexus/` directory (including `meta.json` and all index data). After cleaning, you must re-specify analyze options on the next `analyze` run since stored options are deleted.
 
 | Flag      | Effect                                            |
 | --------- | ------------------------------------------------- |
@@ -237,7 +261,7 @@ $GN unity-ui-trace "Assets/NEON/VeewoUI/Uxml/BarScreen/Patch/PatchItemPreview.ux
 - **"Not inside a git repository"**: Run from a directory inside a git repo
 - **Index is stale after re-analyzing**: Restart Claude Code to reload the MCP server
 - **Embeddings slow**: Omit `--embeddings` (it's off by default) or set `OPENAI_API_KEY` for faster API-based embedding
-- **`analyze --force` hangs or crashes**: Run `$GN clean --force` to remove the corrupted index (sync-manifest is preserved), then `$GN analyze --force` to rebuild. Common corruption signatures: `.gitnexus/csv/` exists but `relations.csv` is missing; `.gitnexus/lbug.wal` exists while `lbug` is only a few KB.
+- **`analyze --force` hangs or crashes**: Run `$GN clean --force` to remove the corrupted index, then `$GN analyze --force` (with your CLI options) to rebuild. Common corruption signatures: `.gitnexus/csv/` exists but `relations.csv` is missing; `.gitnexus/lbug.wal` exists while `lbug` is only a few KB.
 
 ## Runtime-Chain Closure Guard
 

package/vendor/node_modules/node-addon-api/node_addon_api.Makefile

@@ -0,0 +1,6 @@
+# This file is generated by gyp; do not edit.
+
+export builddir_name ?= ./build/../../node_modules/node-addon-api/.
+.PHONY: all
+all:
+	$(MAKE) -C ../../tree-sitter-dart/build node_addon_api_except

package/vendor/node_modules/node-addon-api/node_addon_api.target.mk

@@ -0,0 +1,122 @@
+# This file is generated by gyp; do not edit.
+
+TOOLSET := target
+TARGET := node_addon_api
+DEFS_Debug := \
+	'-DNODE_GYP_MODULE_NAME=node_addon_api' \
+	'-DUSING_UV_SHARED=1' \
+	'-DUSING_V8_SHARED=1' \
+	'-DV8_DEPRECATION_WARNINGS=1' \
+	'-D_GLIBCXX_USE_CXX11_ABI=1' \
+	'-D_FILE_OFFSET_BITS=64' \
+	'-D_DARWIN_USE_64_BIT_INODE=1' \
+	'-D_LARGEFILE_SOURCE' \
+	'-DOPENSSL_NO_PINSHARED' \
+	'-DOPENSSL_THREADS' \
+	'-DDEBUG' \
+	'-D_DEBUG'
+
+# Flags passed to all source files.
+CFLAGS_Debug := \
+	-O0 \
+	-gdwarf-2 \
+	-fno-strict-aliasing \
+	-mmacosx-version-min=13.5 \
+	-arch \
+	arm64 \
+	-Wall \
+	-Wendif-labels \
+	-W \
+	-Wno-unused-parameter
+
+# Flags passed to only C files.
+CFLAGS_C_Debug :=
+
+# Flags passed to only C++ files.
+CFLAGS_CC_Debug := \
+	-std=gnu++20 \
+	-stdlib=libc++ \
+	-fno-rtti \
+	-fno-exceptions
+
+# Flags passed to only ObjC files.
+CFLAGS_OBJC_Debug :=
+
+# Flags passed to only ObjC++ files.
+CFLAGS_OBJCC_Debug :=
+
+INCS_Debug := \
+	-I/Users/nantasmac/Library/Caches/node-gyp/24.15.0/include/node \
+	-I/Users/nantasmac/Library/Caches/node-gyp/24.15.0/src \
+	-I/Users/nantasmac/Library/Caches/node-gyp/24.15.0/deps/openssl/config \
+	-I/Users/nantasmac/Library/Caches/node-gyp/24.15.0/deps/openssl/openssl/include \
+	-I/Users/nantasmac/Library/Caches/node-gyp/24.15.0/deps/uv/include \
+	-I/Users/nantasmac/Library/Caches/node-gyp/24.15.0/deps/zlib \
+	-I/Users/nantasmac/Library/Caches/node-gyp/24.15.0/deps/v8/include
+
+DEFS_Release := \
+	'-DNODE_GYP_MODULE_NAME=node_addon_api' \
+	'-DUSING_UV_SHARED=1' \
+	'-DUSING_V8_SHARED=1' \
+	'-DV8_DEPRECATION_WARNINGS=1' \
+	'-D_GLIBCXX_USE_CXX11_ABI=1' \
+	'-D_FILE_OFFSET_BITS=64' \
+	'-D_DARWIN_USE_64_BIT_INODE=1' \
+	'-D_LARGEFILE_SOURCE' \
+	'-DOPENSSL_NO_PINSHARED' \
+	'-DOPENSSL_THREADS'
+
+# Flags passed to all source files.
+CFLAGS_Release := \
+	-O3 \
+	-gdwarf-2 \
+	-fno-strict-aliasing \
+	-mmacosx-version-min=13.5 \
+	-arch \
+	arm64 \
+	-Wall \
+	-Wendif-labels \
+	-W \
+	-Wno-unused-parameter
+
+# Flags passed to only C files.
+CFLAGS_C_Release :=
+
+# Flags passed to only C++ files.
+CFLAGS_CC_Release := \
+	-std=gnu++20 \
+	-stdlib=libc++ \
+	-fno-rtti \
+	-fno-exceptions
+
+# Flags passed to only ObjC files.
+CFLAGS_OBJC_Release :=
+
+# Flags passed to only ObjC++ files.
+CFLAGS_OBJCC_Release :=
+
+INCS_Release := \
+	-I/Users/nantasmac/Library/Caches/node-gyp/24.15.0/include/node \
+	-I/Users/nantasmac/Library/Caches/node-gyp/24.15.0/src \
+	-I/Users/nantasmac/Library/Caches/node-gyp/24.15.0/deps/openssl/config \
+	-I/Users/nantasmac/Library/Caches/node-gyp/24.15.0/deps/openssl/openssl/include \
+	-I/Users/nantasmac/Library/Caches/node-gyp/24.15.0/deps/uv/include \
+	-I/Users/nantasmac/Library/Caches/node-gyp/24.15.0/deps/zlib \
+	-I/Users/nantasmac/Library/Caches/node-gyp/24.15.0/deps/v8/include
+
+OBJS :=
+
+# Add to the list of files we specially track dependencies for.
+all_deps += $(OBJS)
+
+
+### Rules for final target.
+$(obj).target/../../node_modules/node-addon-api/node_addon_api.stamp: TOOLSET := $(TOOLSET)
+$(obj).target/../../node_modules/node-addon-api/node_addon_api.stamp:  FORCE_DO_CMD
+	$(call do_cmd,touch)
+
+all_deps += $(obj).target/../../node_modules/node-addon-api/node_addon_api.stamp
+# Add target alias
+.PHONY: node_addon_api
+node_addon_api: $(obj).target/../../node_modules/node-addon-api/node_addon_api.stamp
+