refactor!: merge fn into query, fold models into embed --models

CLAUDE.md

@@ -119,7 +119,7 @@ Codegraph is **our own tool**. Use it to analyze this repository before making c
 node src/cli.js build .              # Build/update the graph (incremental)
 node src/cli.js map --limit 20       # Module overview & most-connected nodes
 node src/cli.js stats                # Graph health and quality score
-node src/cli.js fn <name> -T         # Function call chain (callers + callees)
+node src/cli.js query <name> -T      # Function call chain (callers + callees)
 node src/cli.js deps src/<file>.js   # File-level imports and importers
 node src/cli.js diff-impact main     # Impact of current branch vs main
 node src/cli.js complexity -T         # Per-function complexity metrics

FOUNDATION.md

@@ -62,7 +62,7 @@ LLM-powered features (richer embeddings, semantic search, AI-enhanced analysis)
 
 This dual-mode approach is unique in the competitive landscape. Competitors either require cloud APIs for core functionality (code-graph-rag, autodev-codebase) or offer no AI enhancement at all (CKB, axon, arbor). Nobody else offers both modes in one tool.
 
-*Test: does every core command (`build`, `query`, `fn`, `deps`, `impact`, `diff-impact`, `cycles`, `map`) work with zero API keys? Are LLM features additive, never blocking?*
+*Test: does every core command (`build`, `query`, `deps`, `impact`, `diff-impact`, `cycles`, `map`) work with zero API keys? Are LLM features additive, never blocking?*
 
 ### 5. Embeddable first, CLI second
 

README.md

@@ -217,8 +217,8 @@ codegraph explain <function>   # Function summary: signature, calls, callers, te
 
 ```bash
 codegraph impact <file>        # Transitive reverse dependency trace
-codegraph fn <name>            # Function-level: callers, callees, call chain
-codegraph fn <name> --no-tests --depth 5
+codegraph query <name> --no-tests  # Function-level: callers, callees, call chain
+codegraph query <name> --no-tests --depth 5
 codegraph fn-impact <name>     # What functions break if this one changes
 codegraph path <from> <to>     # Shortest path between two symbols (A calls...calls B)
 codegraph path <from> <to> --reverse  # Follow edges backward
@@ -287,7 +287,7 @@ codegraph embed                # Build embeddings (default: nomic-v1.5)
 codegraph embed --model nomic  # Use a different model
 codegraph search "handle authentication"
 codegraph search "parse config" --min-score 0.4 -n 10
-codegraph models               # List available models
+codegraph embed --models       # List available models
 ```
 
 #### Multi-query search
@@ -336,13 +336,13 @@ codegraph registry remove <name>  # Unregister
 | Flag | Description |
 |---|---|
 | `-d, --db <path>` | Custom path to `graph.db` |
-| `-T, --no-tests` | Exclude `.test.`, `.spec.`, `__test__` files (available on `fn`, `fn-impact`, `path`, `context`, `explain`, `where`, `diff-impact`, `search`, `map`, `hotspots`, `roles`, `co-change`, `deps`, `impact`, `complexity`, `communities`, `manifesto`) |
+| `-T, --no-tests` | Exclude `.test.`, `.spec.`, `__test__` files (available on `query`, `fn-impact`, `path`, `context`, `explain`, `where`, `diff-impact`, `search`, `map`, `hotspots`, `roles`, `co-change`, `deps`, `impact`, `complexity`, `communities`, `manifesto`) |
 | `--depth <n>` | Transitive trace depth (default varies by command) |
 | `-j, --json` | Output as JSON |
 | `-v, --verbose` | Enable debug output |
 | `--engine <engine>` | Parser engine: `native`, `wasm`, or `auto` (default: `auto`) |
-| `-k, --kind <kind>` | Filter by kind: `function`, `method`, `class`, `struct`, `enum`, `trait`, `record`, `module` (`fn`, `context`, `search`) |
-| `-f, --file <path>` | Scope to a specific file (`fn`, `context`, `where`) |
+| `-k, --kind <kind>` | Filter by kind: `function`, `method`, `class`, `struct`, `enum`, `trait`, `record`, `module` (`query`, `context`, `search`) |
+| `-f, --file <path>` | Scope to a specific file (`query`, `context`, `where`) |
 | `--rrf-k <n>` | RRF smoothing constant for multi-query search (default 60) |
 
 ## 🌐 Language Support
@@ -485,7 +485,7 @@ This project uses codegraph. The database is at `.codegraph/graph.db`.
 ### Other useful commands
 - `codegraph build .` — rebuild the graph (incremental by default)
 - `codegraph map` — module overview
-- `codegraph fn <name> -T` — function call chain
+- `codegraph query <name> -T` — function call chain
 - `codegraph path <from> <to> -T` — shortest call path between two symbols
 - `codegraph deps <file>` — file-level dependencies
 - `codegraph roles --role dead -T` — find dead code (unreferenced symbols)

scripts/lib/bench-config.js

@@ -70,7 +70,6 @@ export async function resolveBenchmarkSource() {
 				cwd: tmpDir,
 				stdio: 'pipe',
 				timeout: 120_000,
-				shell: true,
 			});
 			break;
 		} catch (err) {

src/cli.js

@@ -26,7 +26,6 @@ import {
   fnImpact,
   impactAnalysis,
   moduleMap,
-  queryName,
   roles,
   stats,
   symbolPath,
@@ -95,16 +94,26 @@ program
 
 program
   .command('query <name>')
-  .description('Find a function/class, show callers and callees')
+  .description('Find a function/class — callers, callees, and transitive call chain')
   .option('-d, --db <path>', 'Path to graph.db')
+  .option('--depth <n>', 'Transitive caller depth', '3')
+  .option('-f, --file <path>', 'Scope search to functions in this file (partial match)')
+  .option('-k, --kind <kind>', 'Filter to a specific symbol kind')
   .option('-T, --no-tests', 'Exclude test/spec files from results')
   .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
   .option('-j, --json', 'Output as JSON')
   .option('--limit <number>', 'Max results to return')
   .option('--offset <number>', 'Skip N results (default: 0)')
   .option('--ndjson', 'Newline-delimited JSON output')
   .action((name, opts) => {
-    queryName(name, opts.db, {
+    if (opts.kind && !ALL_SYMBOL_KINDS.includes(opts.kind)) {
+      console.error(`Invalid kind "${opts.kind}". Valid: ${ALL_SYMBOL_KINDS.join(', ')}`);
+      process.exit(1);
+    }
+    fnDeps(name, opts.db, {
+      depth: parseInt(opts.depth, 10),
+      file: opts.file,
+      kind: opts.kind,
       noTests: resolveNoTests(opts),
       json: opts.json,
       limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
@@ -161,30 +170,6 @@ program
     fileDeps(file, opts.db, { noTests: resolveNoTests(opts), json: opts.json });
   });
 
-program
-  .command('fn <name>')
-  .description('Function-level dependencies: callers, callees, and transitive call chain')
-  .option('-d, --db <path>', 'Path to graph.db')
-  .option('--depth <n>', 'Transitive caller depth', '3')
-  .option('-f, --file <path>', 'Scope search to functions in this file (partial match)')
-  .option('-k, --kind <kind>', 'Filter to a specific symbol kind')
-  .option('-T, --no-tests', 'Exclude test/spec files from results')
-  .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
-  .option('-j, --json', 'Output as JSON')
-  .action((name, opts) => {
-    if (opts.kind && !ALL_SYMBOL_KINDS.includes(opts.kind)) {
-      console.error(`Invalid kind "${opts.kind}". Valid: ${ALL_SYMBOL_KINDS.join(', ')}`);
-      process.exit(1);
-    }
-    fnDeps(name, opts.db, {
-      depth: parseInt(opts.depth, 10),
-      file: opts.file,
-      kind: opts.kind,
-      noTests: resolveNoTests(opts),
-      json: opts.json,
-    });
-  });
-
 program
   .command('fn-impact <name>')
   .description('Function-level impact: what functions break if this one changes')
@@ -489,39 +474,37 @@ registry
 
 // ─── Embedding commands ─────────────────────────────────────────────────
 
-program
-  .command('models')
-  .description('List available embedding models')
-  .action(() => {
-    const defaultModel = config.embeddings?.model || DEFAULT_MODEL;
-    console.log('\nAvailable embedding models:\n');
-    for (const [key, cfg] of Object.entries(MODELS)) {
-      const def = key === defaultModel ? ' (default)' : '';
-      const ctx = cfg.contextWindow ? `${cfg.contextWindow} ctx` : '';
-      console.log(
-        `  ${key.padEnd(12)} ${String(cfg.dim).padStart(4)}d  ${ctx.padEnd(9)} ${cfg.desc}${def}`,
-      );
-    }
-    console.log('\nUsage: codegraph embed --model <name> --strategy <structured|source>');
-    console.log('       codegraph search "query" --model <name>\n');
-  });
-
 program
   .command('embed [dir]')
   .description(
     'Build semantic embeddings for all functions/methods/classes (requires prior `build`)',
   )
   .option(
     '-m, --model <name>',
-    'Embedding model (default from config or minilm). Run `codegraph models` for details',
+    'Embedding model (default from config or minilm). Use `--models` to list available models',
   )
   .option(
     '-s, --strategy <name>',
     `Embedding strategy: ${EMBEDDING_STRATEGIES.join(', ')}. "structured" uses graph context (callers/callees), "source" embeds raw code`,
     'structured',
   )
+  .option('--models', 'List available embedding models and exit')
   .option('-d, --db <path>', 'Path to graph.db')
   .action(async (dir, opts) => {
+    if (opts.models) {
+      const defaultModel = config.embeddings?.model || DEFAULT_MODEL;
+      console.log('\nAvailable embedding models:\n');
+      for (const [key, cfg] of Object.entries(MODELS)) {
+        const def = key === defaultModel ? ' (default)' : '';
+        const ctx = cfg.contextWindow ? `${cfg.contextWindow} ctx` : '';
+        console.log(
+          `  ${key.padEnd(12)} ${String(cfg.dim).padStart(4)}d  ${ctx.padEnd(9)} ${cfg.desc}${def}`,
+        );
+      }
+      console.log('\nUsage: codegraph embed --model <name> --strategy <structured|source>');
+      console.log('       codegraph search "query" --model <name>\n');
+      return;
+    }
     if (!EMBEDDING_STRATEGIES.includes(opts.strategy)) {
       console.error(
         `Unknown strategy: ${opts.strategy}. Available: ${EMBEDDING_STRATEGIES.join(', ')}`,

tests/integration/cli.test.js

@@ -101,9 +101,9 @@ describe('CLI smoke tests', () => {
     expect(data).toHaveProperty('results');
   });
 
-  // ─── Fn ──────────────────────────────────────────────────────────────
-  test('fn --json returns valid JSON with results', () => {
-    const out = run('fn', 'add', '--db', dbPath, '--json');
+  // ─── Query (fn-level) ───────────────────────────────────────────────
+  test('query --json returns fn-level results with depth', () => {
+    const out = run('query', 'add', '--db', dbPath, '--json');
     const data = JSON.parse(out);
     expect(data).toHaveProperty('results');
   });