@optave/codegraph 3.1.0 → 3.1.2

package/src/cli.js

@@ -3,9 +3,10 @@
 import fs from 'node:fs';
 import path from 'node:path';
 import { Command } from 'commander';
-import { audit } from './audit.js';
-import { BATCH_COMMANDS, batch, multiBatchData, splitTargets } from './batch.js';
+import { BATCH_COMMANDS, multiBatchData, splitTargets } from './batch.js';
 import { buildGraph } from './builder.js';
+import { audit } from './commands/audit.js';
+import { batch } from './commands/batch.js';
 import { loadConfig } from './config.js';
 import { findCycles, formatCycles } from './cycles.js';
 import { openReadonlyOrFail } from './db.js';
@@ -24,13 +25,13 @@ import {
   exportMermaid,
   exportNeo4jCSV,
 } from './export.js';
+import { outputResult } from './infrastructure/result-formatter.js';
 import { setVerbose } from './logger.js';
-import { printNdjson } from './paginate.js';
+import { EVERY_SYMBOL_KIND, VALID_ROLES } from './queries.js';
 import {
   children,
   context,
   diffImpact,
-  EVERY_SYMBOL_KIND,
   explain,
   fileDeps,
   fileExports,
@@ -41,9 +42,8 @@ import {
   roles,
   stats,
   symbolPath,
-  VALID_ROLES,
   where,
-} from './queries.js';
+} from './queries-cli.js';
 import {
   listRepos,
   pruneRegistry,
@@ -95,6 +95,17 @@ function resolveNoTests(opts) {
   return config.query?.excludeTests || false;
 }
 
+/** Attach the common query options shared by most analysis commands. */
+const QUERY_OPTS = (cmd) =>
+  cmd
+    .option('-d, --db <path>', 'Path to graph.db')
+    .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');
+
 function formatSize(bytes) {
   if (bytes < 1024) return `${bytes} B`;
   if (bytes < 1024 * 1024) return `${(bytes / 1024).toFixed(1)} KB`;
@@ -122,10 +133,11 @@ program
     });
   });
 
-program
-  .command('query <name>')
-  .description('Function-level dependency chain or shortest path between symbols')
-  .option('-d, --db <path>', 'Path to graph.db')
+QUERY_OPTS(
+  program
+    .command('query <name>')
+    .description('Function-level dependency chain or shortest path between symbols'),
+)
   .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')
@@ -134,12 +146,6 @@ program
   .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) => {
     if (opts.kind && !EVERY_SYMBOL_KIND.includes(opts.kind)) {
       console.error(`Invalid kind "${opts.kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`);
@@ -201,25 +207,17 @@ program
     });
   });
 
-program
-  .command('impact <file>')
-  .description('Show what depends on this file (transitive)')
-  .option('-d, --db <path>', 'Path to graph.db')
-  .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((file, opts) => {
-    impactAnalysis(file, 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,
-    });
+QUERY_OPTS(
+  program.command('impact <file>').description('Show what depends on this file (transitive)'),
+).action((file, opts) => {
+  impactAnalysis(file, 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,
   });
+});
 
 program
   .command('map')
@@ -247,61 +245,43 @@ program
     await stats(opts.db, { noTests: resolveNoTests(opts), json: opts.json });
   });
 
-program
-  .command('deps <file>')
-  .description('Show what this file imports and what imports it')
-  .option('-d, --db <path>', 'Path to graph.db')
-  .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((file, opts) => {
-    fileDeps(file, 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,
-    });
+QUERY_OPTS(
+  program.command('deps <file>').description('Show what this file imports and what imports it'),
+).action((file, opts) => {
+  fileDeps(file, 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,
   });
-
-program
-  .command('exports <file>')
-  .description('Show exported symbols with per-symbol consumers (who calls each export)')
-  .option('-d, --db <path>', 'Path to graph.db')
-  .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')
-  .option('--unused', 'Show only exports with zero consumers')
+});
+
+QUERY_OPTS(
+  program
+    .command('exports <file>')
+    .description('Show exported symbols with per-symbol consumers (who calls each export)'),
+)
+  .option('--unused', 'Show only exports with zero consumers (dead exports)')
   .action((file, opts) => {
     fileExports(file, opts.db, {
       noTests: resolveNoTests(opts),
       json: opts.json,
+      unused: opts.unused || false,
       limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
       offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
       ndjson: opts.ndjson,
-      unused: opts.unused,
     });
   });
 
-program
-  .command('fn-impact <name>')
-  .description('Function-level impact: what functions break if this one changes')
-  .option('-d, --db <path>', 'Path to graph.db')
+QUERY_OPTS(
+  program
+    .command('fn-impact <name>')
+    .description('Function-level impact: what functions break if this one changes'),
+)
   .option('--depth <n>', 'Max transitive depth', '5')
   .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 && !EVERY_SYMBOL_KIND.includes(opts.kind)) {
       console.error(`Invalid kind "${opts.kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`);
@@ -319,21 +299,16 @@ program
     });
   });
 
-program
-  .command('context <name>')
-  .description('Full context for a function: source, deps, callers, tests, signature')
-  .option('-d, --db <path>', 'Path to graph.db')
+QUERY_OPTS(
+  program
+    .command('context <name>')
+    .description('Full context for a function: source, deps, callers, tests, signature'),
+)
   .option('--depth <n>', 'Include callee source up to N levels deep', '0')
   .option('-f, --file <path>', 'Scope search to functions in this file (partial match)')
   .option('-k, --kind <kind>', 'Filter to a specific symbol kind')
   .option('--no-source', 'Metadata only (skip source extraction)')
   .option('--with-test-source', 'Include test source code')
-  .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 && !EVERY_SYMBOL_KIND.includes(opts.kind)) {
       console.error(`Invalid kind "${opts.kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`);
@@ -417,17 +392,12 @@ program
     });
   });
 
-program
-  .command('where [name]')
-  .description('Find where a symbol is defined and used (minimal, fast lookup)')
-  .option('-d, --db <path>', 'Path to graph.db')
+QUERY_OPTS(
+  program
+    .command('where [name]')
+    .description('Find where a symbol is defined and used (minimal, fast lookup)'),
+)
   .option('-f, --file <path>', 'File overview: list symbols, imports, exports')
-  .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 (!name && !opts.file) {
       console.error('Provide a symbol name or use --file <path>');
@@ -448,15 +418,14 @@ program
   .command('diff-impact [ref]')
   .description('Show impact of git changes (unstaged, staged, or vs a ref)')
   .option('-d, --db <path>', 'Path to graph.db')
-  .option('--staged', 'Analyze staged changes instead of unstaged')
-  .option('--depth <n>', 'Max transitive caller depth', '3')
   .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('-f, --format <format>', 'Output format: text, mermaid, json', 'text')
   .option('--limit <number>', 'Max results to return')
   .option('--offset <number>', 'Skip N results (default: 0)')
   .option('--ndjson', 'Newline-delimited JSON output')
+  .option('--staged', 'Analyze staged changes instead of unstaged')
+  .option('--depth <n>', 'Max transitive caller depth', '3')
+  .option('-f, --format <format>', 'Output format: text, mermaid, json', 'text')
   .action((ref, opts) => {
     diffImpact(opts.db, {
       ref,
@@ -501,7 +470,7 @@ program
         console.error(`Invalid kind "${opts.kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`);
         process.exit(1);
       }
-      const { manifesto } = await import('./manifesto.js');
+      const { manifesto } = await import('./commands/manifesto.js');
       manifesto(opts.db, {
         file: opts.file,
         kind: opts.kind,
@@ -515,7 +484,7 @@ program
     }
 
     // Diff predicates mode
-    const { check } = await import('./check.js');
+    const { check } = await import('./commands/check.js');
     check(opts.db, {
       ref,
       staged: opts.staged,
@@ -534,7 +503,7 @@ program
         console.error(`Invalid kind "${opts.kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`);
         process.exit(1);
       }
-      const { manifesto } = await import('./manifesto.js');
+      const { manifesto } = await import('./commands/manifesto.js');
       manifesto(opts.db, {
         file: opts.file,
         kind: opts.kind,
@@ -984,7 +953,7 @@ program
   .option('--offset <number>', 'Skip N results (default: 0)')
   .option('--ndjson', 'Newline-delimited JSON output')
   .action(async (dir, opts) => {
-    const { structureData, formatStructure } = await import('./structure.js');
+    const { structureData, formatStructure } = await import('./commands/structure.js');
     const data = structureData(opts.db, {
       directory: dir,
       depth: opts.depth ? parseInt(opts.depth, 10) : undefined,
@@ -994,11 +963,7 @@ program
       limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
       offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
     });
-    if (opts.ndjson) {
-      printNdjson(data, 'directories');
-    } else if (opts.json) {
-      console.log(JSON.stringify(data, null, 2));
-    } else {
+    if (!outputResult(data, 'directories', opts)) {
       console.log(formatStructure(data));
     }
   });
@@ -1049,8 +1014,8 @@ program
   .option('--offset <number>', 'Skip N results (default: 0)')
   .option('--ndjson', 'Newline-delimited JSON output')
   .action(async (file, opts) => {
-    const { analyzeCoChanges, coChangeData, coChangeTopData, formatCoChange, formatCoChangeTop } =
-      await import('./cochange.js');
+    const { analyzeCoChanges, coChangeData, coChangeTopData } = await import('./cochange.js');
+    const { formatCoChange, formatCoChangeTop } = await import('./commands/cochange.js');
 
     if (opts.analyze) {
       const result = analyzeCoChanges(opts.db, {
@@ -1081,41 +1046,28 @@ program
 
     if (file) {
       const data = coChangeData(file, opts.db, queryOpts);
-      if (opts.ndjson) {
-        printNdjson(data, 'partners');
-      } else if (opts.json) {
-        console.log(JSON.stringify(data, null, 2));
-      } else {
+      if (!outputResult(data, 'partners', opts)) {
         console.log(formatCoChange(data));
       }
     } else {
       const data = coChangeTopData(opts.db, queryOpts);
-      if (opts.ndjson) {
-        printNdjson(data, 'pairs');
-      } else if (opts.json) {
-        console.log(JSON.stringify(data, null, 2));
-      } else {
+      if (!outputResult(data, 'pairs', opts)) {
         console.log(formatCoChangeTop(data));
       }
     }
   });
 
-program
-  .command('flow [name]')
-  .description(
-    'Trace execution flow forward from an entry point (route, command, event) through callees to leaves',
-  )
+QUERY_OPTS(
+  program
+    .command('flow [name]')
+    .description(
+      'Trace execution flow forward from an entry point (route, command, event) through callees to leaves',
+    ),
+)
   .option('--list', 'List all entry points grouped by type')
   .option('--depth <n>', 'Max forward traversal depth', '10')
-  .option('-d, --db <path>', 'Path to graph.db')
   .option('-f, --file <path>', 'Scope to a specific file (partial match)')
   .option('-k, --kind <kind>', 'Filter by 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(async (name, opts) => {
     if (!name && !opts.list) {
       console.error('Provide a function/entry point name or use --list to see all entry points.');
@@ -1125,7 +1077,7 @@ program
       console.error(`Invalid kind "${opts.kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`);
       process.exit(1);
     }
-    const { flow } = await import('./flow.js');
+    const { flow } = await import('./commands/flow.js');
     flow(name, opts.db, {
       list: opts.list,
       depth: parseInt(opts.depth, 10),
@@ -1139,26 +1091,23 @@ program
     });
   });
 
-program
-  .command('sequence <name>')
-  .description('Generate a Mermaid sequence diagram from call graph edges (participants = files)')
+QUERY_OPTS(
+  program
+    .command('sequence <name>')
+    .description(
+      'Generate a Mermaid sequence diagram from call graph edges (participants = files)',
+    ),
+)
   .option('--depth <n>', 'Max forward traversal depth', '10')
   .option('--dataflow', 'Annotate with parameter names and return arrows from dataflow table')
-  .option('-d, --db <path>', 'Path to graph.db')
   .option('-f, --file <path>', 'Scope to a specific file (partial match)')
   .option('-k, --kind <kind>', 'Filter by 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(async (name, opts) => {
     if (opts.kind && !EVERY_SYMBOL_KIND.includes(opts.kind)) {
       console.error(`Invalid kind "${opts.kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`);
       process.exit(1);
     }
-    const { sequence } = await import('./sequence.js');
+    const { sequence } = await import('./commands/sequence.js');
     sequence(name, opts.db, {
       depth: parseInt(opts.depth, 10),
       file: opts.file,
@@ -1172,18 +1121,13 @@ program
     });
   });
 
-program
-  .command('dataflow <name>')
-  .description('Show data flow for a function: parameters, return consumers, mutations')
-  .option('-d, --db <path>', 'Path to graph.db')
+QUERY_OPTS(
+  program
+    .command('dataflow <name>')
+    .description('Show data flow for a function: parameters, return consumers, mutations'),
+)
   .option('-f, --file <path>', 'Scope to file (partial match)')
   .option('-k, --kind <kind>', 'Filter by 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('--ndjson', 'Newline-delimited JSON output')
-  .option('--limit <number>', 'Max results to return')
-  .option('--offset <number>', 'Skip N results (default: 0)')
   .option('--impact', 'Show data-dependent blast radius')
   .option('--depth <n>', 'Max traversal depth', '5')
   .action(async (name, opts) => {
@@ -1191,7 +1135,7 @@ program
       console.error(`Invalid kind "${opts.kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`);
       process.exit(1);
     }
-    const { dataflow } = await import('./dataflow.js');
+    const { dataflow } = await import('./commands/dataflow.js');
     dataflow(name, opts.db, {
       file: opts.file,
       kind: opts.kind,
@@ -1205,25 +1149,16 @@ program
     });
   });
 
-program
-  .command('cfg <name>')
-  .description('Show control flow graph for a function')
-  .option('-d, --db <path>', 'Path to graph.db')
+QUERY_OPTS(program.command('cfg <name>').description('Show control flow graph for a function'))
   .option('--format <fmt>', 'Output format: text, dot, mermaid', 'text')
   .option('-f, --file <path>', 'Scope to file (partial match)')
   .option('-k, --kind <kind>', 'Filter by 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('--ndjson', 'Newline-delimited JSON output')
-  .option('--limit <number>', 'Max results to return')
-  .option('--offset <number>', 'Skip N results (default: 0)')
   .action(async (name, opts) => {
     if (opts.kind && !EVERY_SYMBOL_KIND.includes(opts.kind)) {
       console.error(`Invalid kind "${opts.kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`);
       process.exit(1);
     }
-    const { cfg } = await import('./cfg.js');
+    const { cfg } = await import('./commands/cfg.js');
     cfg(name, opts.db, {
       format: opts.format,
       file: opts.file,
@@ -1260,7 +1195,7 @@ program
       console.error(`Invalid kind "${opts.kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`);
       process.exit(1);
     }
-    const { complexity } = await import('./complexity.js');
+    const { complexity } = await import('./commands/complexity.js');
     complexity(opts.db, {
       target,
       limit: parseInt(opts.limit, 10),
@@ -1276,18 +1211,13 @@ program
     });
   });
 
-program
-  .command('ast [pattern]')
-  .description('Search stored AST nodes (calls, new, string, regex, throw, await) by pattern')
-  .option('-d, --db <path>', 'Path to graph.db')
+QUERY_OPTS(
+  program
+    .command('ast [pattern]')
+    .description('Search stored AST nodes (calls, new, string, regex, throw, await) by pattern'),
+)
   .option('-k, --kind <kind>', 'Filter by AST node kind (call, new, string, regex, throw, await)')
   .option('-f, --file <path>', 'Scope to file (partial match)')
-  .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('--ndjson', 'Newline-delimited JSON output')
-  .option('--limit <number>', 'Max results to return')
-  .option('--offset <number>', 'Skip N results (default: 0)')
   .action(async (pattern, opts) => {
     const { AST_NODE_KINDS, astQuery } = await import('./ast.js');
     if (opts.kind && !AST_NODE_KINDS.includes(opts.kind)) {
@@ -1305,21 +1235,16 @@ program
     });
   });
 
-program
-  .command('communities')
-  .description('Detect natural module boundaries using Louvain community detection')
+QUERY_OPTS(
+  program
+    .command('communities')
+    .description('Detect natural module boundaries using Louvain community detection'),
+)
   .option('--functions', 'Function-level instead of file-level')
   .option('--resolution <n>', 'Louvain resolution parameter (default 1.0)', '1.0')
   .option('--drift', 'Show only drift analysis')
-  .option('-d, --db <path>', 'Path to graph.db')
-  .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(async (opts) => {
-    const { communities } = await import('./communities.js');
+    const { communities } = await import('./commands/communities.js');
     communities(opts.db, {
       functions: opts.functions,
       resolution: parseFloat(opts.resolution),
@@ -1362,7 +1287,7 @@ program
   .action(async (opts) => {
     if (opts.level === 'file' || opts.level === 'directory') {
       // Delegate to hotspots for file/directory level
-      const { hotspotsData, formatHotspots } = await import('./structure.js');
+      const { hotspotsData, formatHotspots } = await import('./commands/structure.js');
       const metric = opts.sort === 'risk' ? 'fan-in' : opts.sort;
       const data = hotspotsData(opts.db, {
         metric,
@@ -1371,11 +1296,7 @@ program
         offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
         noTests: resolveNoTests(opts),
       });
-      if (opts.ndjson) {
-        printNdjson(data, 'hotspots');
-      } else if (opts.json) {
-        console.log(JSON.stringify(data, null, 2));
-      } else {
+      if (!outputResult(data, 'hotspots', opts)) {
         console.log(formatHotspots(data));
       }
       return;
@@ -1398,7 +1319,7 @@ program
         process.exit(1);
       }
     }
-    const { triage } = await import('./triage.js');
+    const { triage } = await import('./commands/triage.js');
     triage(opts.db, {
       limit: parseInt(opts.limit, 10),
       offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
@@ -1426,7 +1347,7 @@ program
   .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
   .option('-j, --json', 'Output as JSON')
   .action(async (target, opts) => {
-    const { owners } = await import('./owners.js');
+    const { owners } = await import('./commands/owners.js');
     owners(opts.db, {
       owner: opts.owner,
       boundary: opts.boundary,
@@ -1446,7 +1367,7 @@ program
   .option('-j, --json', 'Output as JSON')
   .option('-f, --format <format>', 'Output format: text, mermaid, json', 'text')
   .action(async (base, target, opts) => {
-    const { branchCompare } = await import('./branch-compare.js');
+    const { branchCompare } = await import('./commands/branch-compare.js');
     await branchCompare(base, target, {
       engine: program.opts().engine,
       depth: parseInt(opts.depth, 10),

package/src/cochange.js

@@ -10,9 +10,9 @@ import fs from 'node:fs';
 import path from 'node:path';
 import { normalizePath } from './constants.js';
 import { closeDb, findDbPath, initSchema, openDb, openReadonlyOrFail } from './db.js';
+import { isTestFile } from './infrastructure/test-filter.js';
 import { warn } from './logger.js';
 import { paginateResult } from './paginate.js';
-import { isTestFile } from './queries.js';
 
 /**
  * Scan git history and return parsed commit data.
@@ -419,44 +419,6 @@ export function coChangeForFiles(files, db, opts = {}) {
   return results;
 }
 
-/**
- * Format co-change data for CLI output (single file).
- */
-export function formatCoChange(data) {
-  if (data.error) return data.error;
-  if (data.partners.length === 0) return `No co-change partners found for ${data.file}`;
-
-  const lines = [`\nCo-change partners for ${data.file}:\n`];
-  for (const p of data.partners) {
-    const pct = `${(p.jaccard * 100).toFixed(0)}%`.padStart(4);
-    const commits = `${p.commitCount} commits`.padStart(12);
-    lines.push(`  ${pct}  ${commits}  ${p.file}`);
-  }
-  if (data.meta?.analyzedAt) {
-    lines.push(`\n  Analyzed: ${data.meta.analyzedAt} | Window: ${data.meta.since || 'all'}`);
-  }
-  return lines.join('\n');
-}
-
-/**
- * Format top co-change pairs for CLI output (global view).
- */
-export function formatCoChangeTop(data) {
-  if (data.error) return data.error;
-  if (data.pairs.length === 0) return 'No co-change pairs found.';
-
-  const lines = ['\nTop co-change pairs:\n'];
-  for (const p of data.pairs) {
-    const pct = `${(p.jaccard * 100).toFixed(0)}%`.padStart(4);
-    const commits = `${p.commitCount} commits`.padStart(12);
-    lines.push(`  ${pct}  ${commits}  ${p.fileA}  <->  ${p.fileB}`);
-  }
-  if (data.meta?.analyzedAt) {
-    lines.push(`\n  Analyzed: ${data.meta.analyzedAt} | Window: ${data.meta.since || 'all'}`);
-  }
-  return lines.join('\n');
-}
-
 // ─── Internal Helpers ────────────────────────────────────────────────────
 
 function resolveCoChangeFile(db, file) {