refactor: move remaining flat src/ files into subdirectories

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',

src/cli/commands/triage.js

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

src/cli/index.js

@@ -2,9 +2,9 @@ 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 { setVerbose } from '../infrastructure/logger.js';
+import { checkForUpdates, printUpdateNotification } from '../infrastructure/update-check.js';
+import { ConfigError } from '../shared/errors.js';
 import { applyQueryOpts, config, formatSize, resolveNoTests } from './shared/options.js';
 import { outputResult } from './shared/output.js';
 

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());
 

src/commands/check.js

@@ -1,6 +1,6 @@
-import { AnalysisError } from '../errors.js';
 import { checkData } from '../features/check.js';
 import { outputResult } from '../infrastructure/result-formatter.js';
+import { AnalysisError } from '../shared/errors.js';
 
 /**
  * CLI formatter — prints check results and sets exitCode 1 on failure.

src/db/connection.js

@@ -1,8 +1,8 @@
 import fs from 'node:fs';
 import path from 'node:path';
 import Database from 'better-sqlite3';
-import { DbError } from '../errors.js';
-import { warn } from '../logger.js';
+import { warn } from '../infrastructure/logger.js';
+import { DbError } from '../shared/errors.js';
 
 function isProcessAlive(pid) {
   try {

src/db/migrations.js

@@ -1,4 +1,4 @@
-import { debug } from '../logger.js';
+import { debug } from '../infrastructure/logger.js';
 
 // ─── Schema Migrations ─────────────────────────────────────────────────
 export const MIGRATIONS = [

src/db/query-builder.js

@@ -1,5 +1,5 @@
-import { DbError } from '../errors.js';
-import { EVERY_EDGE_KIND } from '../kinds.js';
+import { DbError } from '../shared/errors.js';
+import { EVERY_EDGE_KIND } from '../shared/kinds.js';
 
 // ─── Validation Helpers ─────────────────────────────────────────────
 

src/db/repository/graph-read.js

@@ -1,4 +1,4 @@
-import { CORE_SYMBOL_KINDS } from '../../kinds.js';
+import { CORE_SYMBOL_KINDS } from '../../shared/kinds.js';
 import { cachedStmt } from './cached-stmt.js';
 
 // ─── Statement caches (one prepared statement per db instance) ────────────

src/db/repository/in-memory-repository.js

@@ -1,5 +1,5 @@
-import { ConfigError } from '../../errors.js';
-import { CORE_SYMBOL_KINDS, EVERY_SYMBOL_KIND, VALID_ROLES } from '../../kinds.js';
+import { ConfigError } from '../../shared/errors.js';
+import { CORE_SYMBOL_KINDS, EVERY_SYMBOL_KIND, VALID_ROLES } from '../../shared/kinds.js';
 import { escapeLike } from '../query-builder.js';
 import { Repository } from './base.js';
 

src/db/repository/nodes.js

@@ -1,5 +1,5 @@
-import { ConfigError } from '../../errors.js';
-import { EVERY_SYMBOL_KIND, VALID_ROLES } from '../../kinds.js';
+import { ConfigError } from '../../shared/errors.js';
+import { EVERY_SYMBOL_KIND, VALID_ROLES } from '../../shared/kinds.js';
 import { escapeLike, NodeQuery } from '../query-builder.js';
 import { cachedStmt } from './cached-stmt.js';
 

src/domain/analysis/context.js

@@ -14,7 +14,6 @@ import {
   openReadonlyOrFail,
 } from '../../db/index.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
-import { paginateResult } from '../../paginate.js';
 import {
   createFileLinesReader,
   extractSignature,
@@ -24,6 +23,7 @@ import {
 } from '../../shared/file-utils.js';
 import { resolveMethodViaHierarchy } from '../../shared/hierarchy.js';
 import { normalizeSymbol } from '../../shared/normalize.js';
+import { paginateResult } from '../../shared/paginate.js';
 import { findMatchingNodes } from './symbol-lookup.js';
 
 function explainFileImpl(db, target, getFileLines) {

src/domain/analysis/dependencies.js

@@ -8,9 +8,9 @@ import {
   openReadonlyOrFail,
 } from '../../db/index.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
-import { paginateResult } from '../../paginate.js';
 import { resolveMethodViaHierarchy } from '../../shared/hierarchy.js';
 import { normalizeSymbol } from '../../shared/normalize.js';
+import { paginateResult } from '../../shared/paginate.js';
 import { findMatchingNodes } from './symbol-lookup.js';
 
 export function fileDepsData(file, customDbPath, opts = {}) {

src/domain/analysis/exports.js

@@ -7,12 +7,12 @@ import {
   openReadonlyOrFail,
 } from '../../db/index.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
-import { paginateResult } from '../../paginate.js';
 import {
   createFileLinesReader,
   extractSignature,
   extractSummary,
 } from '../../shared/file-utils.js';
+import { paginateResult } from '../../shared/paginate.js';
 
 export function exportsData(file, customDbPath, opts = {}) {
   const db = openReadonlyOrFail(customDbPath);

src/domain/analysis/impact.js

@@ -1,7 +1,6 @@
 import { execFileSync } from 'node:child_process';
 import fs from 'node:fs';
 import path from 'node:path';
-import { loadConfig } from '../../config.js';
 import {
   findDbPath,
   findDistinctCallers,
@@ -13,9 +12,10 @@ import {
 import { evaluateBoundaries } from '../../features/boundaries.js';
 import { coChangeForFiles } from '../../features/cochange.js';
 import { ownersForFiles } from '../../features/owners.js';
+import { loadConfig } from '../../infrastructure/config.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
-import { paginateResult } from '../../paginate.js';
 import { normalizeSymbol } from '../../shared/normalize.js';
+import { paginateResult } from '../../shared/paginate.js';
 import { findMatchingNodes } from './symbol-lookup.js';
 
 export function impactAnalysisData(file, customDbPath, opts = {}) {

src/domain/analysis/module-map.js

@@ -1,8 +1,8 @@
 import path from 'node:path';
 import { openReadonlyOrFail, testFilterSQL } from '../../db/index.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
-import { LANGUAGE_REGISTRY } from '../../parser.js';
 import { findCycles } from '../graph/cycles.js';
+import { LANGUAGE_REGISTRY } from '../parser.js';
 
 export const FALSE_POSITIVE_NAMES = new Set([
   'run',

src/domain/analysis/roles.js

@@ -1,7 +1,7 @@
 import { openReadonlyOrFail } from '../../db/index.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
-import { paginateResult } from '../../paginate.js';
 import { normalizeSymbol } from '../../shared/normalize.js';
+import { paginateResult } from '../../shared/paginate.js';
 
 export function rolesData(customDbPath, opts = {}) {
   const db = openReadonlyOrFail(customDbPath);

src/domain/analysis/symbol-lookup.js

@@ -14,9 +14,9 @@ import {
   openReadonlyOrFail,
 } from '../../db/index.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
-import { ALL_SYMBOL_KINDS } from '../../kinds.js';
-import { paginateResult } from '../../paginate.js';
+import { ALL_SYMBOL_KINDS } from '../../shared/kinds.js';
 import { getFileHash, normalizeSymbol } from '../../shared/normalize.js';
+import { paginateResult } from '../../shared/paginate.js';
 
 const FUNCTION_KINDS = ['function', 'method', 'class'];
 

src/domain/graph/builder/helpers.js

@@ -6,9 +6,9 @@
 import { createHash } from 'node:crypto';
 import fs from 'node:fs';
 import path from 'node:path';
-import { EXTENSIONS, IGNORE_DIRS } from '../../../constants.js';
 import { purgeFilesData } from '../../../db/index.js';
-import { warn } from '../../../logger.js';
+import { warn } from '../../../infrastructure/logger.js';
+import { EXTENSIONS, IGNORE_DIRS } from '../../../shared/constants.js';
 
 export const BUILTIN_RECEIVERS = new Set([
   'console',

src/domain/graph/builder/incremental.js

@@ -6,9 +6,9 @@
  */
 import fs from 'node:fs';
 import path from 'node:path';
-import { normalizePath } from '../../../constants.js';
-import { warn } from '../../../logger.js';
-import { parseFileIncremental } from '../../../parser.js';
+import { warn } from '../../../infrastructure/logger.js';
+import { normalizePath } from '../../../shared/constants.js';
+import { parseFileIncremental } from '../../parser.js';
 import { computeConfidence, resolveImportPath } from '../resolve.js';
 import { BUILTIN_RECEIVERS, readFileSafe } from './helpers.js';
 

src/domain/graph/builder/pipeline.js

@@ -6,10 +6,10 @@
  */
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
-import { loadConfig } from '../../../config.js';
 import { closeDb, getBuildMeta, initSchema, MIGRATIONS, openDb } from '../../../db/index.js';
-import { info } from '../../../logger.js';
-import { getActiveEngine } from '../../../parser.js';
+import { loadConfig } from '../../../infrastructure/config.js';
+import { info } from '../../../infrastructure/logger.js';
+import { getActiveEngine } from '../../parser.js';
 import { PipelineContext } from './context.js';
 import { loadPathAliases } from './helpers.js';
 import { buildEdges } from './stages/build-edges.js';

src/domain/graph/builder/stages/build-edges.js

@@ -7,7 +7,7 @@
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
 import { getNodeId } from '../../../../db/index.js';
-import { loadNative } from '../../../../native.js';
+import { loadNative } from '../../../../infrastructure/native.js';
 import { computeConfidence } from '../../resolve.js';
 import { BUILTIN_RECEIVERS, batchInsertEdges } from '../helpers.js';
 import { getResolved, isBarrelFile, resolveBarrelExport } from './resolve-imports.js';

src/domain/graph/builder/stages/build-structure.js

@@ -5,8 +5,8 @@
  */
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
-import { normalizePath } from '../../../../constants.js';
-import { debug } from '../../../../logger.js';
+import { debug } from '../../../../infrastructure/logger.js';
+import { normalizePath } from '../../../../shared/constants.js';
 import { readFileSafe } from '../helpers.js';
 
 /**

src/domain/graph/builder/stages/collect-files.js

@@ -5,8 +5,8 @@
  */
 import fs from 'node:fs';
 import path from 'node:path';
-import { normalizePath } from '../../../../constants.js';
-import { info } from '../../../../logger.js';
+import { info } from '../../../../infrastructure/logger.js';
+import { normalizePath } from '../../../../shared/constants.js';
 import { collectFiles as collectFilesUtil } from '../helpers.js';
 
 /**

src/domain/graph/builder/stages/detect-changes.js

@@ -6,11 +6,11 @@
  */
 import fs from 'node:fs';
 import path from 'node:path';
-import { normalizePath } from '../../../../constants.js';
 import { closeDb } from '../../../../db/index.js';
-import { readJournal, writeJournalHeader } from '../../../../journal.js';
-import { debug, info } from '../../../../logger.js';
-import { parseFilesAuto } from '../../../../parser.js';
+import { debug, info } from '../../../../infrastructure/logger.js';
+import { normalizePath } from '../../../../shared/constants.js';
+import { parseFilesAuto } from '../../../parser.js';
+import { readJournal, writeJournalHeader } from '../../journal.js';
 import { fileHash, fileStat, purgeFilesFromGraph, readFileSafe } from '../helpers.js';
 
 /**