@optave/codegraph 3.1.4 → 3.2.0

package/src/cli/commands/owners.js

@@ -1,3 +1,5 @@
+import { collectFile } from '../../db/query-builder.js';
+
 export const command = {
   name: 'owners [target]',
   description: 'Show CODEOWNERS mapping for files and functions',
@@ -5,18 +7,18 @@ export const command = {
     ['-d, --db <path>', 'Path to graph.db'],
     ['--owner <owner>', 'Filter to a specific owner'],
     ['--boundary', 'Show cross-owner boundary edges'],
-    ['-f, --file <path>', 'Scope to a specific file'],
+    ['-f, --file <path>', 'Scope to a specific file (repeatable)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind'],
     ['-T, --no-tests', 'Exclude test/spec files'],
     ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
     ['-j, --json', 'Output as JSON'],
   ],
   async execute([target], opts, ctx) {
-    const { owners } = await import('../../commands/owners.js');
+    const { owners } = await import('../../presentation/owners.js');
     owners(opts.db, {
       owner: opts.owner,
       boundary: opts.boundary,
-      file: opts.file || target,
+      file: opts.file && opts.file.length > 0 ? opts.file : target,
       kind: opts.kind,
       noTests: ctx.resolveNoTests(opts),
       json: opts.json,

package/src/cli/commands/path.js

@@ -1,5 +1,5 @@
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
-import { symbolPath } from '../../queries-cli.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
+import { symbolPath } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'path <from> <to>',

package/src/cli/commands/plot.js

@@ -1,6 +1,6 @@
 import fs from 'node:fs';
 import path from 'node:path';
-import { openReadonlyOrFail } from '../../db.js';
+import { openGraph } from '../shared/open-graph.js';
 
 export const command = {
   name: 'plot',
@@ -22,43 +22,52 @@ export const command = {
     ['--color-by <mode>', 'Color nodes by: kind | role | community | complexity'],
   ],
   async execute(_args, opts, ctx) {
-    const { generatePlotHTML, loadPlotConfig } = await import('../../viewer.js');
+    const { generatePlotHTML, loadPlotConfig } = await import('../../features/graph-enrichment.js');
     const os = await import('node:os');
-    const db = openReadonlyOrFail(opts.db);
+    const { db, close } = openGraph(opts);
 
     let plotCfg;
-    if (opts.config) {
-      try {
-        plotCfg = JSON.parse(fs.readFileSync(opts.config, 'utf-8'));
-      } catch (e) {
-        console.error(`Failed to load config: ${e.message}`);
-        db.close();
-        process.exitCode = 1;
-        return;
+    let html;
+    try {
+      if (opts.config) {
+        try {
+          plotCfg = JSON.parse(fs.readFileSync(opts.config, 'utf-8'));
+        } catch (e) {
+          console.error(`Failed to load config: ${e.message}`);
+          process.exitCode = 1;
+          return;
+        }
+      } else {
+        plotCfg = loadPlotConfig(process.cwd());
+      }
+
+      if (opts.cluster) plotCfg.clusterBy = opts.cluster;
+      if (opts.colorBy) plotCfg.colorBy = opts.colorBy;
+      if (opts.sizeBy) plotCfg.sizeBy = opts.sizeBy;
+      if (opts.seed) plotCfg.seedStrategy = opts.seed;
+      if (opts.seedCount) plotCfg.seedCount = parseInt(opts.seedCount, 10);
+      if (opts.overlay) {
+        const parts = opts.overlay.split(',').map((s) => s.trim());
+        if (!plotCfg.overlays) plotCfg.overlays = {};
+        if (parts.includes('complexity')) plotCfg.overlays.complexity = true;
+        if (parts.includes('risk')) plotCfg.overlays.risk = true;
       }
-    } else {
-      plotCfg = loadPlotConfig(process.cwd());
-    }
 
-    if (opts.cluster) plotCfg.clusterBy = opts.cluster;
-    if (opts.colorBy) plotCfg.colorBy = opts.colorBy;
-    if (opts.sizeBy) plotCfg.sizeBy = opts.sizeBy;
-    if (opts.seed) plotCfg.seedStrategy = opts.seed;
-    if (opts.seedCount) plotCfg.seedCount = parseInt(opts.seedCount, 10);
-    if (opts.overlay) {
-      const parts = opts.overlay.split(',').map((s) => s.trim());
-      if (!plotCfg.overlays) plotCfg.overlays = {};
-      if (parts.includes('complexity')) plotCfg.overlays.complexity = true;
-      if (parts.includes('risk')) plotCfg.overlays.risk = true;
+      html = generatePlotHTML(db, {
+        fileLevel: !opts.functions,
+        noTests: ctx.resolveNoTests(opts),
+        minConfidence: parseFloat(opts.minConfidence),
+        config: plotCfg,
+      });
+    } finally {
+      close();
     }
 
-    const html = generatePlotHTML(db, {
-      fileLevel: !opts.functions,
-      noTests: ctx.resolveNoTests(opts),
-      minConfidence: parseFloat(opts.minConfidence),
-      config: plotCfg,
-    });
-    db.close();
+    if (!html) {
+      console.error('generatePlotHTML returned no output');
+      process.exitCode = 1;
+      return;
+    }
 
     const outPath = opts.output || path.join(os.tmpdir(), `codegraph-plot-${Date.now()}.html`);
     fs.writeFileSync(outPath, html, 'utf-8');

package/src/cli/commands/query.js

@@ -1,5 +1,6 @@
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
-import { fnDeps, symbolPath } from '../../queries-cli.js';
+import { collectFile } from '../../db/query-builder.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
+import { fnDeps, symbolPath } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'query <name>',
@@ -7,7 +8,11 @@ export const command = {
   queryOpts: true,
   options: [
     ['--depth <n>', 'Transitive caller depth', '3'],
-    ['-f, --file <path>', 'Scope search to functions in this file (partial match)'],
+    [
+      '-f, --file <path>',
+      'Scope search to functions in this file (partial match, repeatable)',
+      collectFile,
+    ],
     ['-k, --kind <kind>', 'Filter to a specific symbol kind'],
     ['--path <to>', 'Path mode: find shortest path to <to>'],
     ['--kinds <kinds>', 'Path mode: comma-separated edge kinds to follow (default: calls)'],
@@ -38,11 +43,7 @@ export const command = {
         depth: parseInt(opts.depth, 10),
         file: opts.file,
         kind: opts.kind,
-        noTests: ctx.resolveNoTests(opts),
-        json: opts.json,
-        limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-        offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-        ndjson: opts.ndjson,
+        ...ctx.resolveQueryOpts(opts),
       });
     }
   },

package/src/cli/commands/registry.js

@@ -1,13 +1,13 @@
 import fs from 'node:fs';
 import path from 'node:path';
-import { ConfigError } from '../../errors.js';
 import {
   listRepos,
   pruneRegistry,
   REGISTRY_PATH,
   registerRepo,
   unregisterRepo,
-} from '../../registry.js';
+} from '../../infrastructure/registry.js';
+import { ConfigError } from '../../shared/errors.js';
 
 export const command = {
   name: 'registry',

package/src/cli/commands/roles.js

@@ -1,5 +1,6 @@
-import { VALID_ROLES } from '../../queries.js';
-import { roles } from '../../queries-cli.js';
+import { collectFile } from '../../db/query-builder.js';
+import { VALID_ROLES } from '../../domain/queries.js';
+import { roles } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'roles',
@@ -7,7 +8,7 @@ export const command = {
   options: [
     ['-d, --db <path>', 'Path to graph.db'],
     ['--role <role>', `Filter by role (${VALID_ROLES.join(', ')})`],
-    ['-f, --file <path>', 'Scope to a specific file (partial match)'],
+    ['-f, --file <path>', 'Scope to a specific file (partial match, repeatable)', collectFile],
     ['-T, --no-tests', 'Exclude test/spec files'],
     ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
     ['-j, --json', 'Output as JSON'],
@@ -24,11 +25,7 @@ export const command = {
     roles(opts.db, {
       role: opts.role,
       file: opts.file,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      ndjson: opts.ndjson,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/search.js

@@ -1,4 +1,5 @@
-import { search } from '../../embeddings/index.js';
+import { collectFile } from '../../db/query-builder.js';
+import { search } from '../../domain/search/index.js';
 
 export const command = {
   name: 'search <query>',
@@ -11,7 +12,7 @@ export const command = {
     ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
     ['--min-score <score>', 'Minimum similarity threshold', '0.2'],
     ['-k, --kind <kind>', 'Filter by kind: function, method, class'],
-    ['--file <pattern>', 'Filter by file path pattern'],
+    ['--file <pattern>', 'Filter by file path pattern (repeatable)', collectFile],
     ['--rrf-k <number>', 'RRF k parameter for multi-query ranking', '60'],
     ['--mode <mode>', 'Search mode: hybrid, semantic, keyword (default: hybrid)'],
     ['-j, --json', 'Output as JSON'],
@@ -25,6 +26,11 @@ export const command = {
     }
   },
   async execute([query], opts, ctx) {
+    // --file collects into an array; pass single element unwrapped for single
+    // value, or pass the raw array for multi-file scoping.
+    const fileArr = opts.file || [];
+    const filePattern =
+      fileArr.length === 1 ? fileArr[0] : fileArr.length > 1 ? fileArr : undefined;
     await search(query, opts.db, {
       limit: parseInt(opts.limit, 10),
       offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
@@ -32,7 +38,7 @@ export const command = {
       minScore: parseFloat(opts.minScore),
       model: opts.model,
       kind: opts.kind,
-      filePattern: opts.file,
+      filePattern,
       rrfK: parseInt(opts.rrfK, 10),
       mode: opts.mode,
       json: opts.json,

package/src/cli/commands/sequence.js

@@ -1,4 +1,5 @@
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
+import { collectFile } from '../../db/query-builder.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 
 export const command = {
   name: 'sequence <name>',
@@ -7,7 +8,7 @@ export const command = {
   options: [
     ['--depth <n>', 'Max forward traversal depth', '10'],
     ['--dataflow', 'Annotate with parameter names and return arrows from dataflow table'],
-    ['-f, --file <path>', 'Scope to a specific file (partial match)'],
+    ['-f, --file <path>', 'Scope to a specific file (partial match, repeatable)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind'],
   ],
   validate([_name], opts) {
@@ -16,17 +17,13 @@ export const command = {
     }
   },
   async execute([name], opts, ctx) {
-    const { sequence } = await import('../../commands/sequence.js');
+    const { sequence } = await import('../../presentation/sequence.js');
     sequence(name, opts.db, {
       depth: parseInt(opts.depth, 10),
       file: opts.file,
       kind: opts.kind,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
       dataflow: opts.dataflow,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      ndjson: opts.ndjson,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/snapshot.js

@@ -1,4 +1,9 @@
-import { snapshotDelete, snapshotList, snapshotRestore, snapshotSave } from '../../snapshot.js';
+import {
+  snapshotDelete,
+  snapshotList,
+  snapshotRestore,
+  snapshotSave,
+} from '../../features/snapshot.js';
 
 export const command = {
   name: 'snapshot',

package/src/cli/commands/stats.js

@@ -1,4 +1,4 @@
-import { stats } from '../../queries-cli.js';
+import { stats } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'stats',

package/src/cli/commands/structure.js

@@ -15,15 +15,16 @@ export const command = {
     ['--ndjson', 'Newline-delimited JSON output'],
   ],
   async execute([dir], opts, ctx) {
-    const { structureData, formatStructure } = await import('../../commands/structure.js');
+    const { structureData, formatStructure } = await import('../../presentation/structure.js');
+    const qOpts = ctx.resolveQueryOpts(opts);
     const data = structureData(opts.db, {
       directory: dir,
       depth: opts.depth ? parseInt(opts.depth, 10) : undefined,
       sort: opts.sort,
       full: opts.full,
-      noTests: ctx.resolveNoTests(opts),
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+      noTests: qOpts.noTests,
+      limit: qOpts.limit,
+      offset: qOpts.offset,
     });
     if (!ctx.outputResult(data, 'directories', opts)) {
       console.log(formatStructure(data));

package/src/cli/commands/triage.js

@@ -1,5 +1,39 @@
-import { ConfigError } from '../../errors.js';
-import { EVERY_SYMBOL_KIND, VALID_ROLES } from '../../queries.js';
+import { collectFile } from '../../db/query-builder.js';
+import { EVERY_SYMBOL_KIND, VALID_ROLES } from '../../domain/queries.js';
+import { ConfigError } from '../../shared/errors.js';
+
+function validateFilters(opts) {
+  if (opts.kind && !EVERY_SYMBOL_KIND.includes(opts.kind)) {
+    throw new ConfigError(`Invalid kind "${opts.kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`);
+  }
+  if (opts.role && !VALID_ROLES.includes(opts.role)) {
+    throw new ConfigError(`Invalid role "${opts.role}". Valid: ${VALID_ROLES.join(', ')}`);
+  }
+}
+
+function parseWeights(raw) {
+  if (!raw) return undefined;
+  try {
+    return JSON.parse(raw);
+  } catch (err) {
+    throw new ConfigError('Invalid --weights JSON', { cause: err });
+  }
+}
+
+async function runHotspots(opts, ctx) {
+  const { hotspotsData, formatHotspots } = await import('../../presentation/structure.js');
+  const metric = opts.sort === 'risk' ? 'fan-in' : opts.sort;
+  const data = hotspotsData(opts.db, {
+    metric,
+    level: opts.level,
+    limit: parseInt(opts.limit, 10),
+    offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+    noTests: ctx.resolveNoTests(opts),
+  });
+  if (!ctx.outputResult(data, 'hotspots', opts)) {
+    console.log(formatHotspots(data));
+  }
+}
 
 export const command = {
   name: 'triage',
@@ -20,7 +54,7 @@ export const command = {
     ],
     ['--min-score <score>', 'Only show symbols with risk score >= threshold'],
     ['--role <role>', 'Filter by role (entry, core, utility, adapter, leaf, dead)'],
-    ['-f, --file <path>', 'Scope to a specific file (partial match)'],
+    ['-f, --file <path>', 'Scope to a specific file (partial match, repeatable)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind (function, method, class)'],
     ['-T, --no-tests', 'Exclude test/spec files from results'],
     ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
@@ -31,36 +65,13 @@ export const command = {
   ],
   async execute(_args, opts, ctx) {
     if (opts.level === 'file' || opts.level === 'directory') {
-      const { hotspotsData, formatHotspots } = await import('../../commands/structure.js');
-      const metric = opts.sort === 'risk' ? 'fan-in' : opts.sort;
-      const data = hotspotsData(opts.db, {
-        metric,
-        level: opts.level,
-        limit: parseInt(opts.limit, 10),
-        offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-        noTests: ctx.resolveNoTests(opts),
-      });
-      if (!ctx.outputResult(data, 'hotspots', opts)) {
-        console.log(formatHotspots(data));
-      }
+      await runHotspots(opts, ctx);
       return;
     }
 
-    if (opts.kind && !EVERY_SYMBOL_KIND.includes(opts.kind)) {
-      throw new ConfigError(`Invalid kind "${opts.kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`);
-    }
-    if (opts.role && !VALID_ROLES.includes(opts.role)) {
-      throw new ConfigError(`Invalid role "${opts.role}". Valid: ${VALID_ROLES.join(', ')}`);
-    }
-    let weights;
-    if (opts.weights) {
-      try {
-        weights = JSON.parse(opts.weights);
-      } catch (err) {
-        throw new ConfigError('Invalid --weights JSON', { cause: err });
-      }
-    }
-    const { triage } = await import('../../commands/triage.js');
+    validateFilters(opts);
+    const weights = parseWeights(opts.weights);
+    const { triage } = await import('../../presentation/triage.js');
     triage(opts.db, {
       limit: parseInt(opts.limit, 10),
       offset: opts.offset ? parseInt(opts.offset, 10) : undefined,

package/src/cli/commands/watch.js

@@ -1,5 +1,5 @@
 import path from 'node:path';
-import { watchProject } from '../../watcher.js';
+import { watchProject } from '../../domain/graph/watcher.js';
 
 export const command = {
   name: 'watch [dir]',

package/src/cli/commands/where.js

@@ -1,4 +1,4 @@
-import { where } from '../../queries-cli.js';
+import { where } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'where [name]',
@@ -14,11 +14,7 @@ export const command = {
     const target = opts.file || name;
     where(target, opts.db, {
       file: !!opts.file,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      ndjson: opts.ndjson,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/index.js

@@ -2,10 +2,16 @@ import fs from 'node:fs';
 import path from 'node:path';
 import { pathToFileURL } from 'node:url';
 import { Command } from 'commander';
-import { ConfigError } from '../errors.js';
-import { setVerbose } from '../logger.js';
-import { checkForUpdates, printUpdateNotification } from '../update-check.js';
-import { applyQueryOpts, config, formatSize, resolveNoTests } from './shared/options.js';
+import { setVerbose } from '../infrastructure/logger.js';
+import { checkForUpdates, printUpdateNotification } from '../infrastructure/update-check.js';
+import { ConfigError } from '../shared/errors.js';
+import {
+  applyQueryOpts,
+  config,
+  formatSize,
+  resolveNoTests,
+  resolveQueryOpts,
+} from './shared/options.js';
 import { outputResult } from './shared/output.js';
 
 const __cliDir = path.dirname(new URL(import.meta.url).pathname.replace(/^\/([A-Z]:)/i, '$1'));
@@ -35,7 +41,7 @@ program
   });
 
 /** Shared context passed to every command's execute(). */
-const ctx = { config, resolveNoTests, formatSize, outputResult, program };
+const ctx = { config, resolveNoTests, resolveQueryOpts, formatSize, outputResult, program };
 
 /**
  * Register a command definition onto a Commander parent.

package/src/cli/shared/open-graph.js

@@ -0,0 +1,13 @@
+import { openReadonlyOrFail } from '../../db/index.js';
+
+/**
+ * Open the graph database in readonly mode with a clean close() handle.
+ *
+ * @param {object} [opts]
+ * @param {string} [opts.db] - Custom path to graph.db
+ * @returns {{ db: import('better-sqlite3').Database, close: () => void }}
+ */
+export function openGraph(opts = {}) {
+  const db = openReadonlyOrFail(opts.db);
+  return { db, close: () => db.close() };
+}

package/src/cli/shared/options.js

@@ -1,4 +1,4 @@
-import { loadConfig } from '../../config.js';
+import { loadConfig } from '../../infrastructure/config.js';
 
 const config = loadConfig(process.cwd());
 
@@ -15,7 +15,9 @@ export function applyQueryOpts(cmd) {
     .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('--ndjson', 'Newline-delimited JSON output')
+    .option('--table', 'Output as aligned table')
+    .option('--csv', 'Output as CSV');
 }
 
 /**
@@ -30,6 +32,24 @@ export function resolveNoTests(opts) {
   return config.query?.excludeTests || false;
 }
 
+/**
+ * Extract the common query option fields shared by most analysis commands.
+ *
+ * Spreads cleanly into per-command option objects:
+ *   `{ ...resolveQueryOpts(opts), depth: parseInt(opts.depth, 10) }`
+ */
+export function resolveQueryOpts(opts) {
+  return {
+    noTests: resolveNoTests(opts),
+    json: opts.json,
+    ndjson: opts.ndjson,
+    table: opts.table,
+    csv: opts.csv,
+    limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
+    offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+  };
+}
+
 export function formatSize(bytes) {
   if (bytes < 1024) return `${bytes} B`;
   if (bytes < 1024 * 1024) return `${(bytes / 1024).toFixed(1)} KB`;

package/src/cli.js

@@ -1,7 +1,7 @@
 #!/usr/bin/env node
 
 import { run } from './cli/index.js';
-import { CodegraphError } from './errors.js';
+import { CodegraphError } from './shared/errors.js';
 
 run().catch((err) => {
   if (err instanceof CodegraphError) {