refactor: reorganize src/ into domain/, features/, presentation/ layers (#456)

* refactor: reorganize src/ into domain/, features/, presentation/ layers

Move source files into a domain-driven directory structure:
- src/domain/ — core graph building, queries, analysis, search (embeddings)
- src/features/ — composable feature modules (audit, check, complexity, etc.)
- src/presentation/ — CLI formatting and output rendering
- src/db/ — database layer (db.js → db/index.js)

All 199 files updated with corrected import paths.
1858 tests pass, 0 cycles, all manifesto rules green.

Impact: 22 functions changed, 5 affected

* docs: update CLAUDE.md architecture table for new directory structure

Update file paths in the architecture table to reflect the domain/,
features/, presentation/, db/ reorganization. Addresses Greptile review.

Author: carlos-alm

CLAUDE.md

@@ -17,7 +17,7 @@
 
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
-import { bulkNodeIdsByFile } from '../db.js';
+import { bulkNodeIdsByFile } from '../db/index.js';
 import { debug } from '../logger.js';
 import { computeLOCMetrics, computeMaintainabilityIndex } from './metrics.js';
 import {

src/ast-analysis/engine.js

@@ -1,6 +1,6 @@
 import { audit } from '../../commands/audit.js';
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
-import { explain } from '../../queries-cli.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
+import { explain } from '../../presentation/queries-cli.js';
 
 export const command = {
   name: 'audit <target>',

src/cli/commands/audit.js

@@ -1,8 +1,8 @@
 import fs from 'node:fs';
-import { BATCH_COMMANDS, multiBatchData, splitTargets } from '../../batch.js';
 import { batch } from '../../commands/batch.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 import { ConfigError } from '../../errors.js';
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
+import { BATCH_COMMANDS, multiBatchData, splitTargets } from '../../features/batch.js';
 
 export const command = {
   name: 'batch <command> [targets...]',

src/cli/commands/batch.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]',

src/cli/commands/build.js

@@ -1,4 +1,4 @@
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 
 export const command = {
   name: 'cfg <name>',

src/cli/commands/cfg.js

@@ -1,5 +1,5 @@
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 import { ConfigError } from '../../errors.js';
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
 
 export const command = {
   name: 'check [ref]',

src/cli/commands/check.js

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

src/cli/commands/children.js

@@ -1,4 +1,4 @@
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 
 export const command = {
   name: 'complexity [target]',

src/cli/commands/complexity.js

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