@optave/codegraph 3.1.4 → 3.2.0

package/src/cli/commands/build.js

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

package/src/cli/commands/cfg.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: 'cfg <name>',
@@ -6,7 +7,7 @@ export const command = {
   queryOpts: true,
   options: [
     ['--format <fmt>', 'Output format: text, dot, mermaid', 'text'],
-    ['-f, --file <path>', 'Scope to file (partial match)'],
+    ['-f, --file <path>', 'Scope to file (partial match, repeatable)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind'],
   ],
   validate([_name], opts) {
@@ -15,16 +16,12 @@ export const command = {
     }
   },
   async execute([name], opts, ctx) {
-    const { cfg } = await import('../../commands/cfg.js');
+    const { cfg } = await import('../../presentation/cfg.js');
     cfg(name, opts.db, {
       format: opts.format,
       file: opts.file,
       kind: opts.kind,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
-      ndjson: opts.ndjson,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/check.js

@@ -1,5 +1,23 @@
-import { ConfigError } from '../../errors.js';
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
+import { collectFile } from '../../db/query-builder.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
+import { ConfigError } from '../../shared/errors.js';
+import { config } from '../shared/options.js';
+
+function validateKind(kind) {
+  if (kind && !EVERY_SYMBOL_KIND.includes(kind)) {
+    throw new ConfigError(`Invalid kind "${kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`);
+  }
+}
+
+async function runManifesto(opts, qOpts) {
+  validateKind(opts.kind);
+  const { manifesto } = await import('../../presentation/manifesto.js');
+  manifesto(opts.db, {
+    file: opts.file,
+    kind: opts.kind,
+    ...qOpts,
+  });
+}
 
 export const command = {
   name: 'check [ref]',
@@ -14,7 +32,7 @@ export const command = {
     ['--signatures', 'Assert no function declaration lines were modified'],
     ['--boundaries', 'Assert no cross-owner boundary violations'],
     ['--depth <n>', 'Max BFS depth for blast radius (default: 3)'],
-    ['-f, --file <path>', 'Scope to file (partial match, manifesto mode)'],
+    ['-f, --file <path>', 'Scope to file (partial match, repeatable, manifesto mode)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind (manifesto mode)'],
     ['-T, --no-tests', 'Exclude test/spec files from results'],
     ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
@@ -25,27 +43,14 @@ export const command = {
   ],
   async execute([ref], opts, ctx) {
     const isDiffMode = ref || opts.staged;
+    const qOpts = ctx.resolveQueryOpts(opts);
 
     if (!isDiffMode && !opts.rules) {
-      if (opts.kind && !EVERY_SYMBOL_KIND.includes(opts.kind)) {
-        throw new ConfigError(
-          `Invalid kind "${opts.kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`,
-        );
-      }
-      const { manifesto } = await import('../../commands/manifesto.js');
-      manifesto(opts.db, {
-        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,
-      });
+      await runManifesto(opts, qOpts);
       return;
     }
 
-    const { check } = await import('../../commands/check.js');
+    const { check } = await import('../../presentation/check.js');
     check(opts.db, {
       ref,
       staged: opts.staged,
@@ -54,26 +59,13 @@ export const command = {
       signatures: opts.signatures || undefined,
       boundaries: opts.boundaries || undefined,
       depth: opts.depth ? parseInt(opts.depth, 10) : undefined,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
+      noTests: qOpts.noTests,
+      json: qOpts.json,
+      config,
     });
 
     if (opts.rules) {
-      if (opts.kind && !EVERY_SYMBOL_KIND.includes(opts.kind)) {
-        throw new ConfigError(
-          `Invalid kind "${opts.kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`,
-        );
-      }
-      const { manifesto } = await import('../../commands/manifesto.js');
-      manifesto(opts.db, {
-        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,
-      });
+      await runManifesto(opts, qOpts);
     }
   },
 };

package/src/cli/commands/children.js

@@ -1,12 +1,17 @@
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
-import { children } from '../../queries-cli.js';
+import { collectFile } from '../../db/query-builder.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
+import { children } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'children <name>',
   description: 'List parameters, properties, and constants of a symbol',
   options: [
     ['-d, --db <path>', 'Path to graph.db'],
-    ['-f, --file <path>', 'Scope search to symbols in this file (partial match)'],
+    [
+      '-f, --file <path>',
+      'Scope search to symbols in this file (partial match, repeatable)',
+      collectFile,
+    ],
     ['-k, --kind <kind>', 'Filter to a specific symbol kind'],
     ['-T, --no-tests', 'Exclude test/spec files from results'],
     ['-j, --json', 'Output as JSON'],
@@ -22,10 +27,7 @@ export const command = {
     children(name, opts.db, {
       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,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/co-change.js

@@ -1,4 +1,4 @@
-import { AnalysisError } from '../../errors.js';
+import { AnalysisError } from '../../shared/errors.js';
 
 export const command = {
   name: 'co-change [file]',
@@ -19,8 +19,10 @@ export const command = {
     ['--ndjson', 'Newline-delimited JSON output'],
   ],
   async execute([file], opts, ctx) {
-    const { analyzeCoChanges, coChangeData, coChangeTopData } = await import('../../cochange.js');
-    const { formatCoChange, formatCoChangeTop } = await import('../../commands/cochange.js');
+    const { analyzeCoChanges, coChangeData, coChangeTopData } = await import(
+      '../../features/cochange.js'
+    );
+    const { formatCoChange, formatCoChangeTop } = await import('../../presentation/cochange.js');
 
     if (opts.analyze) {
       const result = analyzeCoChanges(opts.db, {

package/src/cli/commands/communities.js

@@ -8,16 +8,12 @@ export const command = {
     ['--drift', 'Show only drift analysis'],
   ],
   async execute(_args, opts, ctx) {
-    const { communities } = await import('../../commands/communities.js');
+    const { communities } = await import('../../presentation/communities.js');
     communities(opts.db, {
       functions: opts.functions,
       resolution: parseFloat(opts.resolution),
       drift: opts.drift,
-      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/complexity.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: 'complexity [target]',
@@ -13,7 +14,7 @@ export const command = {
     ],
     ['--above-threshold', 'Only functions exceeding warn thresholds'],
     ['--health', 'Show health metrics (Halstead, MI) columns'],
-    ['-f, --file <path>', 'Scope to file (partial match)'],
+    ['-f, --file <path>', 'Scope to file (partial match, repeatable)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind'],
     ['-T, --no-tests', 'Exclude test/spec files from results'],
     ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
@@ -27,7 +28,7 @@ export const command = {
     }
   },
   async execute([target], opts, ctx) {
-    const { complexity } = await import('../../commands/complexity.js');
+    const { complexity } = await import('../../presentation/complexity.js');
     complexity(opts.db, {
       target,
       limit: parseInt(opts.limit, 10),
@@ -40,6 +41,7 @@ export const command = {
       noTests: ctx.resolveNoTests(opts),
       json: opts.json,
       ndjson: opts.ndjson,
+      config: ctx.config,
     });
   },
 };

package/src/cli/commands/context.js

@@ -1,5 +1,6 @@
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
-import { context } from '../../queries-cli.js';
+import { collectFile } from '../../db/query-builder.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
+import { context } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'context <name>',
@@ -7,7 +8,11 @@ export const command = {
   queryOpts: true,
   options: [
     ['--depth <n>', 'Include callee source up to N levels deep', '0'],
-    ['-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'],
     ['--no-source', 'Metadata only (skip source extraction)'],
     ['--with-test-source', 'Include test source code'],
@@ -23,12 +28,8 @@ export const command = {
       file: opts.file,
       kind: opts.kind,
       noSource: !opts.source,
-      noTests: ctx.resolveNoTests(opts),
       includeTests: opts.withTestSource,
-      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/cycles.js

@@ -1,5 +1,5 @@
-import { findCycles, formatCycles } from '../../cycles.js';
-import { openReadonlyOrFail } from '../../db.js';
+import { findCycles, formatCycles } from '../../domain/graph/cycles.js';
+import { openGraph } from '../shared/open-graph.js';
 
 export const command = {
   name: 'cycles',
@@ -12,12 +12,16 @@ export const command = {
     ['-j, --json', 'Output as JSON'],
   ],
   execute(_args, opts, ctx) {
-    const db = openReadonlyOrFail(opts.db);
-    const cycles = findCycles(db, {
-      fileLevel: !opts.functions,
-      noTests: ctx.resolveNoTests(opts),
-    });
-    db.close();
+    const { db, close } = openGraph(opts);
+    let cycles;
+    try {
+      cycles = findCycles(db, {
+        fileLevel: !opts.functions,
+        noTests: ctx.resolveNoTests(opts),
+      });
+    } finally {
+      close();
+    }
 
     if (opts.json) {
       console.log(JSON.stringify({ cycles, count: cycles.length }, null, 2));

package/src/cli/commands/dataflow.js

@@ -1,11 +1,12 @@
-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: 'dataflow <name>',
   description: 'Show data flow for a function: parameters, return consumers, mutations',
   queryOpts: true,
   options: [
-    ['-f, --file <path>', 'Scope to file (partial match)'],
+    ['-f, --file <path>', 'Scope to file (partial match, repeatable)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind'],
     ['--impact', 'Show data-dependent blast radius'],
     ['--depth <n>', 'Max traversal depth', '5'],
@@ -16,17 +17,13 @@ export const command = {
     }
   },
   async execute([name], opts, ctx) {
-    const { dataflow } = await import('../../commands/dataflow.js');
+    const { dataflow } = await import('../../presentation/dataflow.js');
     dataflow(name, opts.db, {
       file: opts.file,
       kind: opts.kind,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
-      ndjson: opts.ndjson,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
       impact: opts.impact,
       depth: parseInt(opts.depth, 10),
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/deps.js

@@ -1,16 +1,17 @@
-import { fileDeps } from '../../queries-cli.js';
+import { brief } from '../../presentation/brief.js';
+import { fileDeps } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'deps <file>',
   description: 'Show what this file imports and what imports it',
   queryOpts: true,
+  options: [['--brief', 'Compact output with symbol roles, caller counts, and risk tier']],
   execute([file], opts, ctx) {
-    fileDeps(file, opts.db, {
-      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,
-    });
+    const qOpts = ctx.resolveQueryOpts(opts);
+    if (opts.brief) {
+      brief(file, opts.db, qOpts);
+    } else {
+      fileDeps(file, opts.db, qOpts);
+    }
   },
 };

package/src/cli/commands/diff-impact.js

@@ -1,4 +1,4 @@
-import { diffImpact } from '../../queries-cli.js';
+import { diffImpact } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'diff-impact [ref]',
@@ -19,12 +19,8 @@ export const command = {
       ref,
       staged: opts.staged,
       depth: parseInt(opts.depth, 10),
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
       format: opts.format,
-      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/embed.js

@@ -1,5 +1,5 @@
 import path from 'node:path';
-import { buildEmbeddings, DEFAULT_MODEL, EMBEDDING_STRATEGIES } from '../../embeddings/index.js';
+import { buildEmbeddings, DEFAULT_MODEL, EMBEDDING_STRATEGIES } from '../../domain/search/index.js';
 
 export const command = {
   name: 'embed [dir]',

package/src/cli/commands/export.js

@@ -1,5 +1,4 @@
 import fs from 'node:fs';
-import { openReadonlyOrFail } from '../../db.js';
 import {
   exportDOT,
   exportGraphML,
@@ -7,7 +6,8 @@ import {
   exportJSON,
   exportMermaid,
   exportNeo4jCSV,
-} from '../../export.js';
+} from '../../features/export.js';
+import { openGraph } from '../shared/open-graph.js';
 
 export const command = {
   name: 'export',
@@ -23,7 +23,7 @@ export const command = {
     ['-o, --output <file>', 'Write to file instead of stdout'],
   ],
   execute(_args, opts, ctx) {
-    const db = openReadonlyOrFail(opts.db);
+    const { db, close } = openGraph(opts);
     const exportOpts = {
       fileLevel: !opts.functions,
       noTests: ctx.resolveNoTests(opts),
@@ -32,38 +32,41 @@ export const command = {
     };
 
     let output;
-    switch (opts.format) {
-      case 'mermaid':
-        output = exportMermaid(db, exportOpts);
-        break;
-      case 'json':
-        output = JSON.stringify(exportJSON(db, exportOpts), null, 2);
-        break;
-      case 'graphml':
-        output = exportGraphML(db, exportOpts);
-        break;
-      case 'graphson':
-        output = JSON.stringify(exportGraphSON(db, exportOpts), null, 2);
-        break;
-      case 'neo4j': {
-        const csv = exportNeo4jCSV(db, exportOpts);
-        if (opts.output) {
-          const base = opts.output.replace(/\.[^.]+$/, '') || opts.output;
-          fs.writeFileSync(`${base}-nodes.csv`, csv.nodes, 'utf-8');
-          fs.writeFileSync(`${base}-relationships.csv`, csv.relationships, 'utf-8');
-          db.close();
-          console.log(`Exported to ${base}-nodes.csv and ${base}-relationships.csv`);
-          return;
+    try {
+      switch (opts.format) {
+        case 'mermaid':
+          output = exportMermaid(db, exportOpts);
+          break;
+        case 'json':
+          output = JSON.stringify(exportJSON(db, exportOpts), null, 2);
+          break;
+        case 'graphml':
+          output = exportGraphML(db, exportOpts);
+          break;
+        case 'graphson':
+          output = JSON.stringify(exportGraphSON(db, exportOpts), null, 2);
+          break;
+        case 'neo4j': {
+          const csv = exportNeo4jCSV(db, exportOpts);
+          if (opts.output) {
+            const base = opts.output.replace(/\.[^.]+$/, '') || opts.output;
+            fs.writeFileSync(`${base}-nodes.csv`, csv.nodes, 'utf-8');
+            fs.writeFileSync(`${base}-relationships.csv`, csv.relationships, 'utf-8');
+            console.log(`Exported to ${base}-nodes.csv and ${base}-relationships.csv`);
+          } else {
+            output = `--- nodes.csv ---\n${csv.nodes}\n\n--- relationships.csv ---\n${csv.relationships}`;
+          }
+          break;
         }
-        output = `--- nodes.csv ---\n${csv.nodes}\n\n--- relationships.csv ---\n${csv.relationships}`;
-        break;
+        default:
+          output = exportDOT(db, exportOpts);
+          break;
       }
-      default:
-        output = exportDOT(db, exportOpts);
-        break;
+    } finally {
+      close();
     }
 
-    db.close();
+    if (output === undefined) return;
 
     if (opts.output) {
       fs.writeFileSync(opts.output, output, 'utf-8');

package/src/cli/commands/exports.js

@@ -1,4 +1,4 @@
-import { fileExports } from '../../queries-cli.js';
+import { fileExports } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'exports <file>',
@@ -7,12 +7,8 @@ export const command = {
   options: [['--unused', 'Show only exports with zero consumers (dead exports)']],
   execute([file], opts, ctx) {
     fileExports(file, opts.db, {
-      noTests: ctx.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,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/flow.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: 'flow [name]',
@@ -8,7 +9,7 @@ export const command = {
   options: [
     ['--list', 'List all entry points grouped by type'],
     ['--depth <n>', 'Max forward traversal depth', '10'],
-    ['-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) {
@@ -20,17 +21,13 @@ export const command = {
     }
   },
   async execute([name], opts, ctx) {
-    const { flow } = await import('../../commands/flow.js');
+    const { flow } = await import('../../presentation/flow.js');
     flow(name, opts.db, {
       list: opts.list,
       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/fn-impact.js

@@ -1,5 +1,6 @@
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
-import { fnImpact } from '../../queries-cli.js';
+import { collectFile } from '../../db/query-builder.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
+import { fnImpact } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'fn-impact <name>',
@@ -7,7 +8,11 @@ export const command = {
   queryOpts: true,
   options: [
     ['--depth <n>', 'Max transitive depth', '5'],
-    ['-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'],
   ],
   validate([_name], opts) {
@@ -20,11 +25,7 @@ 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/impact.js

@@ -1,4 +1,4 @@
-import { impactAnalysis } from '../../queries-cli.js';
+import { impactAnalysis } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'impact <file>',
@@ -6,11 +6,7 @@ export const command = {
   queryOpts: true,
   execute([file], opts, ctx) {
     impactAnalysis(file, opts.db, {
-      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/info.js

@@ -3,9 +3,9 @@ export const command = {
   description: 'Show codegraph engine info and diagnostics',
   async execute(_args, _opts, ctx) {
     const { getNativePackageVersion, isNativeAvailable, loadNative } = await import(
-      '../../native.js'
+      '../../infrastructure/native.js'
     );
-    const { getActiveEngine } = await import('../../parser.js');
+    const { getActiveEngine } = await import('../../domain/parser.js');
 
     const engine = ctx.program.opts().engine;
     const { name: activeName, version: activeVersion } = getActiveEngine({ engine });

package/src/cli/commands/map.js

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

package/src/cli/commands/mcp.js

@@ -7,7 +7,7 @@ export const command = {
     ['--repos <names>', 'Comma-separated list of allowed repo names (restricts access)'],
   ],
   async execute(_args, opts) {
-    const { startMCPServer } = await import('../../mcp.js');
+    const { startMCPServer } = await import('../../mcp/index.js');
     const mcpOpts = {};
     mcpOpts.multiRepo = opts.multiRepo || !!opts.repos;
     if (opts.repos) {

package/src/cli/commands/models.js

@@ -1,4 +1,4 @@
-import { DEFAULT_MODEL, MODELS } from '../../embeddings/index.js';
+import { DEFAULT_MODEL, MODELS } from '../../domain/search/index.js';
 
 export const command = {
   name: 'models',