[PatrickSys]

New projects default to local, model-free indexing and search. Setup configures Claude Code, Codex, Cursor and OpenCode together, preserves unrelated settings, and launches the installed package directly through Node.

Writers publish complete index generations and readers retain a consistent snapshot. Search checks nominated source excerpts, relationship checks distinguish excluded or unavailable targets from missing imports, and watcher exclusions are relative to the project. Windows ticket replacement retries are limited to the exact owned rename failure reproduced with ordinary Node read handles; the generic config writer and failed-read behavior are unchanged. Existing semantic indexes retain their recorded mode, with directed imports and re-exports available up to three hops.

Includes the commits from #138, #139 and #142. PR140's extra clients and HTTP setup remain separate.

Validation:

• Windows full suite on the complete final tree: 1,309 passed with one existing skip across 122 test files. The normal pre-push hook passed without bypassing checks. All 54 focused init checks also passed. CI passed on that same head.
• Normal clean local-tarball install with scripts enabled and no optional-dependency omission. All 392 packaged artifacts match the build, including 106 executable files and grammars; neither optional model nor LanceDB package resolves. Actual installed four-client init preserved existing registrations and produced a byte-identical rerun on a Windows path containing spaces, &, % and Unicode.
• A native Codex consumer made the five original Express MCP searches and read source for four answers; the graph question retains its explicit limitation. The other three native applications were not opened.
• The 21 queries were frozen before the repairs: Express found an expected file in the top five for 8/10, Hono for 6/11. All 21 completed without tool errors. This is a file-hit proxy, not answer accuracy or a comparison with another tool.
• The installed candidate migrated the preserved Hono index. Sampled peak server RSS was about 1.38 GB for Hono and 302 MB for warm Express, with a 100 ms polling delay. These are observations, not unique physical memory or a controlled performance comparison.

Limits: all five native searches reported low confidence. Ranked search does not establish the globally least-connected module. Earlier Windows runs included an uncaptured SDK response, baseline timeout, ticket-open error and a separate confinement error; their causes are not established by later passing runs. The ordinary-read-handle rename failure was reproduced separately and has a bounded ticket-only repair. No stable release, universal error-free operation or complete product acceptance is claimed.

[PatrickSys]

Every get_symbol_references call now reads and Tree-sitter-parses every indexed file: the chunk prefilter is gone, and findIdentifierOccurrences parses without a cheap text check first. Testing the word on the current file text before parsing would keep current-source truth without the full scan.

• codebase-context/src/core/symbol-references.ts

  Lines 123 to 145 in 129ad6b

  	const candidateFiles = new Map<string, string>();
  	for (const chunkRaw of chunks) {
  	const chunk = chunkRaw as IndexedChunk;
  	const absPath = resolveAbsoluteChunkPath(rootPath, chunk);
  	if (!absPath) {
  	return {
  	status: 'error',
  	message:
  	'Indexed source location is invalid. Refresh the index before trusting reference results.'
  	};
  	}
  	const relPath = path.relative(rootPath, absPath).replace(/\\/g, '/');
  	candidateFiles.set(relPath, absPath);
  	}
  	let realRootPath: string;
  	try {
  	realRootPath = await fs.realpath(rootPath);
  	} catch {
  	return { status: 'error', message: 'Selected project path is missing or unreadable.' };
  	}
  	for (const [relativePath, absolutePath] of candidateFiles) {

• codebase-context/src/core/symbol-references.ts

  Line 173 in 129ad6b

  const occurrences = await findIdentifierOccurrences(

• codebase-context/src/utils/tree-sitter.ts

  Line 455 in 129ad6b

  tree = parser.parse(content);

[PatrickSys]

If any of the ~30 search candidates was edited after indexing (before the watcher catches up, or from the CLI), search throws IndexCorruptedError, starts a full re-index and returns status: indexing, while get_code_relationships keeps answering and just marks drifted edges stale. Dropping or flagging the drifted candidate would keep search working.

• codebase-context/src/core/search.ts

  Lines 230 to 266 in 129ad6b

  	private async validateCandidateSources(
  	chunks: Iterable<CodeChunk>,
  	checkedSources: Map<string, string>
  	): Promise<void> {
  	if (!this.sourceManifest) {
  	throw new IndexCorruptedError('Source manifest is unavailable. Full rebuild required.');
  	}
  	let realRootPath: string | undefined;
  	for (const chunk of chunks) {
  	const sourcePath = this.getIndexedSourcePath(chunk);
  	const sourceKey = path.resolve(this.rootPath, chunk.filePath);
  	if (checkedSources.has(sourceKey)) continue;
  	const relativePath = path.relative(this.rootPath, sourcePath).replace(/\\/g, '/');
  	const expectedHash = this.sourceManifest.files[relativePath];
  	if (typeof expectedHash !== 'string') {
  	throw new IndexCorruptedError(
  	'Indexed source is absent from its manifest. Full rebuild required.'
  	);
  	}
  	try {
  	realRootPath ??= await fs.realpath(this.rootPath);
  	const realSourcePath = await fs.realpath(sourcePath);
  	if (!isPathWithin(realRootPath, realSourcePath)) {
  	throw new Error('Source resolves outside the selected project');
  	}
  	if (!(await fs.stat(realSourcePath)).isFile()) {
  	throw new Error('Source is not a regular file');
  	}
  	const content = await fs.readFile(realSourcePath, 'utf-8');
  	if (hashFileContent(content) !== expectedHash) throw new Error('Source content changed');
  	checkedSources.set(sourceKey, content);
  	} catch {
  	throw new IndexCorruptedError(
  	`Indexed source is changed or unreadable (${relativePath}). Full rebuild required.`
  	);
  	}
  	}

• codebase-context/src/core/search.ts

  Line 1035 in 129ad6b

  await this.validateCandidateSources(

• codebase-context/src/tools/search-codebase.ts

  Lines 225 to 227 in 129ad6b

  	if (error instanceof IndexCorruptedError) {
  	console.error('[Auto-Heal] Index corrupted. Triggering background re-index...');
  	void ctx.performIndexing();

• codebase-context/src/tools/get-code-relationships.ts

  Line 26 in 129ad6b

  const collectionKeys = ['paths', 'unresolved', 'staleEdges', 'staleUnresolvedEdges'];

[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-10-30T05:17:59.226580Z	51305e2	Draft marked ready

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review" or "@codex security review".

Codex reacts with 👀 while any review is running, comments if it has suggestions, and reacts with 👍 once all reviews finish with no findings.

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: c536317677

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[chatgpt-codex-connector]

Apply watcher exclusions relative to the selected project root

When a checkout is beneath an ancestor named worktrees, .worktrees, build, or another excluded directory, this predicate matches that ancestor in every absolute path, including rootPath itself. For example, both /home/user/worktrees/my-project and its src/main.ts are marked ignored, so the watcher never triggers incremental refreshes for that project. Apply exclusions to paths relative to rootPath, exempting the selected root itself, so excluded directories inside the project are skipped without disabling watching based on the checkout's location.

Useful? React with 👍 / 👎.

[greptile-apps]

Confidence Score: 5/5

[High impact] The PR appears safe to merge; the excluded-import warning is fixed and no new actionable issues were found.

Summary

This PR makes new indexes model-free, configures four coding tools, and publishes complete index builds while readers keep one consistent view.

• Setup configures selected coding tools to launch the project package directly.
• Fresh projects build keyword indexes without downloading models.
• Index updates publish complete generations while readers keep one snapshot.
• Search checks nominated excerpts against current source before ranking results.
• A new tool follows verified imports and re-exports between source files.
• Indexed code chunks keep their source spans and clearer symbol ownership.

Diagram

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  Sources[Project source] --> Build[Build a complete generation]
  Build --> Publish[Replace index metadata]
  Publish --> Latest[Latest committed generation]
  Latest --> Pin[Reader pins one generation]
  Pin --> Check[Check current source evidence]
  Check --> Results[Search or relationship results]

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_{Reviews (3) · Last reviewed commit: "Preserve saved Codex settings during set..." · Reviewed by Greptile}