refactor: move remaining flat src/ files into subdirectories (#458)

* 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.

* refactor: move remaining flat src/ files into subdirectories

Move 12 remaining files out of flat src/ so only cli.js and index.js
remain as entry points:
- config, logger, native, registry, update-check → infrastructure/
- constants, errors, kinds, paginate → shared/
- parser → domain/
- journal, change-journal → domain/graph/

Update all import paths across src/ and tests/.
Update CLAUDE.md architecture table to match.

Impact: 9 functions changed, 17 affected

* style: fix import ordering after file moves

Author: carlos-alm

CLAUDE.md

@@ -42,21 +42,28 @@ JS source is plain JavaScript (ES modules) in `src/`. No transpilation step. The
 |------|------|
 | `cli.js` | Commander CLI entry point (`bin.codegraph`) |
 | `index.js` | Programmatic API exports |
-| `parser.js` | tree-sitter WASM wrapper; `LANGUAGE_REGISTRY` + per-language extractors for functions, classes, methods, imports, exports, call sites |
-| `config.js` | `.codegraphrc.json` loading, env overrides, `apiKeyCommand` secret resolution |
-| `constants.js` | `EXTENSIONS` (derived from parser registry) and `IGNORE_DIRS` constants |
-| `native.js` | Native napi-rs addon loader with WASM fallback |
-| `registry.js` | Global repo registry (`~/.codegraph/registry.json`) for multi-repo MCP |
-| `paginate.js` | Pagination helpers for bounded query results |
-| `logger.js` | Structured logging (`warn`, `debug`, `info`, `error`) |
+| **`shared/`** | **Cross-cutting constants and utilities** |
+| `shared/constants.js` | `EXTENSIONS` (derived from parser registry) and `IGNORE_DIRS` constants |
+| `shared/errors.js` | Domain error hierarchy (`CodegraphError`, `ConfigError`, `ParseError`, etc.) |
+| `shared/kinds.js` | Symbol and edge kind constants (`CORE_SYMBOL_KINDS`, `EVERY_SYMBOL_KIND`, `VALID_ROLES`) |
+| `shared/paginate.js` | Pagination helpers for bounded query results |
+| **`infrastructure/`** | **Platform and I/O plumbing** |
+| `infrastructure/config.js` | `.codegraphrc.json` loading, env overrides, `apiKeyCommand` secret resolution |
+| `infrastructure/logger.js` | Structured logging (`warn`, `debug`, `info`, `error`) |
+| `infrastructure/native.js` | Native napi-rs addon loader with WASM fallback |
+| `infrastructure/registry.js` | Global repo registry (`~/.codegraph/registry.json`) for multi-repo MCP |
+| `infrastructure/update-check.js` | npm update availability check |
 | **`db/`** | **Database layer** |
 | `db/index.js` | SQLite schema and operations (`better-sqlite3`) |
 | **`domain/`** | **Core domain logic** |
-| `domain/queries.js` | Query functions: symbol search, file deps, impact analysis, diff-impact; `SYMBOL_KINDS` constant defines all node kinds |
+| `domain/parser.js` | tree-sitter WASM wrapper; `LANGUAGE_REGISTRY` + per-language extractors for functions, classes, methods, imports, exports, call sites |
+| `domain/queries.js` | Query functions: symbol search, file deps, impact analysis, diff-impact |
 | `domain/graph/builder.js` | Graph building: file collection, parsing, import resolution, incremental hashing |
 | `domain/graph/cycles.js` | Circular dependency detection (delegates to `graph/` subsystem) |
 | `domain/graph/resolve.js` | Import resolution (supports native batch mode) |
 | `domain/graph/watcher.js` | Watch mode for incremental rebuilds |
+| `domain/graph/journal.js` | Change journal for incremental builds |
+| `domain/graph/change-journal.js` | Change event tracking (NDJSON) |
 | `domain/analysis/` | Query-layer analysis: context, dependencies, exports, impact, module-map, roles, symbol-lookup |
 | `domain/search/` | Embedding subsystem: model management, vector generation, semantic/keyword/hybrid search, CLI formatting |
 | **`features/`** | **Composable feature modules** |
@@ -87,7 +94,7 @@ JS source is plain JavaScript (ES modules) in `src/`. No transpilation step. The
 - **Dual-engine architecture:** Native Rust parsing via napi-rs (`crates/codegraph-core/`) with automatic fallback to WASM. Controlled by `--engine native|wasm|auto` (default: `auto`)
 - Platform-specific prebuilt binaries published as optional npm packages (`@optave/codegraph-{platform}-{arch}`)
 - WASM grammars are built from devDeps on `npm install` (via `prepare` script) and not committed to git — used as fallback when native addon is unavailable
-- **Language parser registry:** `LANGUAGE_REGISTRY` in `parser.js` is the single source of truth for all supported languages — maps each language to `{ id, extensions, grammarFile, extractor, required }`. `EXTENSIONS` in `constants.js` is derived from the registry. Adding a new language requires one registry entry + extractor function
+- **Language parser registry:** `LANGUAGE_REGISTRY` in `domain/parser.js` is the single source of truth for all supported languages — maps each language to `{ id, extensions, grammarFile, extractor, required }`. `EXTENSIONS` in `shared/constants.js` is derived from the registry. Adding a new language requires one registry entry + extractor function
 - **Node kinds:** `SYMBOL_KINDS` in `domain/queries.js` lists all valid kinds: `function`, `method`, `class`, `interface`, `type`, `struct`, `enum`, `trait`, `record`, `module`. Language-specific types use their native kind (e.g. Go structs → `struct`, Rust traits → `trait`, Ruby modules → `module`) rather than mapping everything to `class`/`interface`
 - `@huggingface/transformers` and `@modelcontextprotocol/sdk` are optional dependencies, lazy-loaded
 - Non-required parsers (all except JS/TS/TSX) fail gracefully if their WASM grammar is unavailable

src/ast-analysis/engine.js

@@ -18,7 +18,7 @@
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
 import { bulkNodeIdsByFile } from '../db/index.js';
-import { debug } from '../logger.js';
+import { debug } from '../infrastructure/logger.js';
 import { computeLOCMetrics, computeMaintainabilityIndex } from './metrics.js';
 import {
   AST_TYPE_MAPS,
@@ -45,7 +45,7 @@ const WALK_EXTENSIONS = buildExtensionSet(AST_TYPE_MAPS);
 
 let _parserModule = null;
 async function getParserModule() {
-  if (!_parserModule) _parserModule = await import('../parser.js');
+  if (!_parserModule) _parserModule = await import('../domain/parser.js');
   return _parserModule;
 }
 

src/ast-analysis/shared.js

@@ -2,8 +2,8 @@
  * Shared utilities for AST analysis modules (complexity, CFG, dataflow, AST nodes).
  */
 
-import { ConfigError } from '../errors.js';
-import { LANGUAGE_REGISTRY } from '../parser.js';
+import { LANGUAGE_REGISTRY } from '../domain/parser.js';
+import { ConfigError } from '../shared/errors.js';
 
 // ─── Generic Rule Factory ─────────────────────────────────────────────────
 

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) {

src/cli/commands/ast.js

@@ -1,4 +1,4 @@
-import { ConfigError } from '../../errors.js';
+import { ConfigError } from '../../shared/errors.js';
 
 export const command = {
   name: 'ast [pattern]',

src/cli/commands/batch.js

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

src/cli/commands/check.js

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

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]',

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 });

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',