refactor!: consolidate MCP tools and CLI commands

CLAUDE.md

@@ -126,7 +126,8 @@ 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 query <a> --path <b> -T  # Shortest path between two symbols
 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

README.md

@@ -237,12 +237,12 @@ 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>         # 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
-codegraph path <from> <to> --max-depth 5 --kinds calls,imports
+codegraph query <from> --path <to>     # Shortest path between two symbols (A calls...calls B)
+codegraph query <from> --path <to> --reverse  # Follow edges backward
+codegraph query <from> --path <to> --depth 5 --kinds calls,imports
 codegraph diff-impact          # Impact of unstaged git changes
 codegraph diff-impact --staged # Impact of staged changes
 codegraph diff-impact HEAD~3   # Impact vs a specific ref
@@ -566,8 +566,8 @@ 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 path <from> <to> -T` — shortest call path between two symbols
+- `codegraph query <name> -T` — function call chain (callers + callees)
+- `codegraph query <from> --path <to> -T` — shortest call path between two symbols
 - `codegraph deps <file>` — file-level dependencies
 - `codegraph roles --role dead -T` — find dead code (unreferenced symbols)
 - `codegraph roles --role core -T` — find core symbols (high fan-in)

src/batch.js

@@ -15,7 +15,6 @@ import {
   fnDepsData,
   fnImpactData,
   impactAnalysisData,
-  queryNameData,
   whereData,
 } from './queries.js';
 
@@ -32,8 +31,7 @@ export const BATCH_COMMANDS = {
   context: { fn: contextData, sig: 'name' },
   explain: { fn: explainData, sig: 'target' },
   where: { fn: whereData, sig: 'target' },
-  query: { fn: queryNameData, sig: 'name' },
-  fn: { fn: fnDepsData, sig: 'name' },
+  query: { fn: fnDepsData, sig: 'name' },
   impact: { fn: impactAnalysisData, sig: 'file' },
   deps: { fn: fileDepsData, sig: 'file' },
   flow: { fn: flowData, sig: 'name' },

src/cli.js

@@ -29,7 +29,6 @@ import {
   fnImpact,
   impactAnalysis,
   moduleMap,
-  queryName,
   roles,
   stats,
   symbolPath,
@@ -106,22 +105,50 @@ program
 
 program
   .command('query <name>')
-  .description('Find a function/class, show callers and callees')
+  .description('Function-level dependency chain or shortest path between symbols')
   .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('--path <to>', 'Path mode: find shortest path to <to>')
+  .option('--kinds <kinds>', 'Path mode: comma-separated edge kinds to follow (default: calls)')
+  .option('--reverse', 'Path mode: follow edges backward')
+  .option('--from-file <path>', 'Path mode: disambiguate source symbol by file')
+  .option('--to-file <path>', 'Path mode: disambiguate target symbol by file')
   .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, {
-      noTests: resolveNoTests(opts),
-      json: opts.json,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      ndjson: opts.ndjson,
-    });
+    if (opts.kind && !ALL_SYMBOL_KINDS.includes(opts.kind)) {
+      console.error(`Invalid kind "${opts.kind}". Valid: ${ALL_SYMBOL_KINDS.join(', ')}`);
+      process.exit(1);
+    }
+    if (opts.path) {
+      symbolPath(name, opts.path, opts.db, {
+        maxDepth: opts.depth ? parseInt(opts.depth, 10) : 10,
+        edgeKinds: opts.kinds ? opts.kinds.split(',').map((s) => s.trim()) : undefined,
+        reverse: opts.reverse,
+        fromFile: opts.fromFile,
+        toFile: opts.toFile,
+        kind: opts.kind,
+        noTests: resolveNoTests(opts),
+        json: opts.json,
+      });
+    } else {
+      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,
+        offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+        ndjson: opts.ndjson,
+      });
+    }
   });
 
 program
@@ -190,36 +217,6 @@ program
     });
   });
 
-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')
-  .option('--limit <number>', 'Max results to return')
-  .option('--offset <number>', 'Skip N results (default: 0)')
-  .option('--ndjson', 'Newline-delimited JSON output')
-  .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,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      ndjson: opts.ndjson,
-    });
-  });
-
 program
   .command('fn-impact <name>')
   .description('Function-level impact: what functions break if this one changes')
@@ -250,36 +247,6 @@ program
     });
   });
 
-program
-  .command('path <from> <to>')
-  .description('Find shortest path between two symbols (A calls...calls B)')
-  .option('-d, --db <path>', 'Path to graph.db')
-  .option('--max-depth <n>', 'Maximum BFS depth', '10')
-  .option('--kinds <kinds>', 'Comma-separated edge kinds to follow (default: calls)')
-  .option('--reverse', 'Follow edges backward (B is called by...called by A)')
-  .option('--from-file <path>', 'Disambiguate source symbol by file (partial match)')
-  .option('--to-file <path>', 'Disambiguate target symbol by file (partial match)')
-  .option('-k, --kind <kind>', 'Filter both symbols by 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((from, to, opts) => {
-    if (opts.kind && !ALL_SYMBOL_KINDS.includes(opts.kind)) {
-      console.error(`Invalid kind "${opts.kind}". Valid: ${ALL_SYMBOL_KINDS.join(', ')}`);
-      process.exit(1);
-    }
-    symbolPath(from, to, opts.db, {
-      maxDepth: parseInt(opts.maxDepth, 10),
-      edgeKinds: opts.kinds ? opts.kinds.split(',').map((s) => s.trim()) : undefined,
-      reverse: opts.reverse,
-      fromFile: opts.fromFile,
-      toFile: opts.toFile,
-      kind: opts.kind,
-      noTests: resolveNoTests(opts),
-      json: opts.json,
-    });
-  });
-
 program
   .command('context <name>')
   .description('Full context for a function: source, deps, callers, tests, signature')
@@ -980,7 +947,6 @@ program
   .option('--ndjson', 'Newline-delimited JSON output')
   .option('--limit <number>', 'Max results to return')
   .option('--offset <number>', 'Skip N results (default: 0)')
-  .option('--path <target>', 'Find data flow path to <target>')
   .option('--impact', 'Show data-dependent blast radius')
   .option('--depth <n>', 'Max traversal depth', '5')
   .action(async (name, opts) => {
@@ -997,7 +963,6 @@ program
       ndjson: opts.ndjson,
       limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
       offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      path: opts.path,
       impact: opts.impact,
       depth: opts.depth,
     });

src/dataflow.js

@@ -1089,9 +1089,6 @@ export function dataflowImpactData(name, customDbPath, opts = {}) {
  * CLI display for dataflow command.
  */
 export function dataflow(name, customDbPath, opts = {}) {
-  if (opts.path) {
-    return dataflowPath(name, opts.path, customDbPath, opts);
-  }
   if (opts.impact) {
     return dataflowImpact(name, customDbPath, opts);
   }
@@ -1168,40 +1165,6 @@ export function dataflow(name, customDbPath, opts = {}) {
   }
 }
 
-/**
- * CLI display for dataflow --path.
- */
-function dataflowPath(from, to, customDbPath, opts = {}) {
-  const data = dataflowPathData(from, to, customDbPath, {
-    noTests: opts.noTests,
-    maxDepth: opts.depth ? Number(opts.depth) : 10,
-  });
-
-  if (opts.json) {
-    console.log(JSON.stringify(data, null, 2));
-    return;
-  }
-
-  if (data.warning) {
-    console.log(`⚠  ${data.warning}`);
-    return;
-  }
-  if (!data.found) {
-    console.log(data.error || `No data flow path found from "${from}" to "${to}".`);
-    return;
-  }
-
-  console.log(
-    `\nData flow path: ${from} → ${to}  (${data.hops} hop${data.hops !== 1 ? 's' : ''})\n`,
-  );
-  for (let i = 0; i < data.path.length; i++) {
-    const p = data.path[i];
-    const prefix = i === 0 ? '  ●' : `  ${'│ '.repeat(i - 1)}├─`;
-    const edge = p.edgeKind ? ` [${p.edgeKind}]` : '';
-    console.log(`${prefix} ${p.name} (${p.file}:${p.line})${edge}`);
-  }
-}
-
 /**
  * CLI display for dataflow --impact.
  */