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

CLAUDE.md

@@ -38,47 +38,57 @@ npm run release:dry-run          # Preview what release would do without writing
 
 JS source is plain JavaScript (ES modules) in `src/`. No transpilation step. The Rust native engine lives in `crates/codegraph-core/`.
 
-| File | Role |
+| Path | Role |
 |------|------|
 | `cli.js` | Commander CLI entry point (`bin.codegraph`) |
 | `index.js` | Programmatic API exports |
-| `builder.js` | Graph building: file collection, parsing, import resolution, incremental hashing |
 | `parser.js` | tree-sitter WASM wrapper; `LANGUAGE_REGISTRY` + per-language extractors for functions, classes, methods, imports, exports, call sites |
-| `queries.js` | Query functions: symbol search, file deps, impact analysis, diff-impact; `SYMBOL_KINDS` constant defines all node kinds |
-| `embeddings/` | Embedding subsystem: model management, vector generation, semantic/keyword/hybrid search, CLI formatting |
-| `db.js` | SQLite schema and operations (`better-sqlite3`) |
-| `mcp.js` | MCP server exposing graph queries to AI agents; single-repo by default, `--multi-repo` to enable cross-repo access |
-| `graph/` | Unified graph model: `CodeGraph` class (`model.js`), algorithms (Tarjan SCC, Louvain, BFS, shortest path, centrality), classifiers (role, risk), builders (dependency, structure, temporal) |
-| `cycles.js` | Circular dependency detection (delegates to `graph/` subsystem) |
-| `export.js` | Graph export orchestration: loads data from DB, delegates to `presentation/export.js` serializers |
-| `presentation/` | Pure output formatting: `viewer.js` (HTML renderer), `export.js` (DOT/Mermaid/GraphML/Neo4j serializers), `sequence-renderer.js` (Mermaid sequence diagrams), `table.js` (CLI table formatting), `result-formatter.js` (JSON/NDJSON output) |
-| `watcher.js` | Watch mode for incremental rebuilds |
 | `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 |
-| `resolve.js` | Import resolution (supports native batch mode) |
-| `ast-analysis/` | Unified AST analysis framework: shared DFS walker (`visitor.js`), engine orchestrator (`engine.js`), extracted metrics (`metrics.js`), and pluggable visitors for complexity, dataflow, and AST-store |
-| `complexity.js` | Cognitive, cyclomatic, Halstead, MI computation from AST; `complexity` CLI command |
-| `communities.js` | Louvain community detection, drift analysis (delegates to `graph/` subsystem) |
-| `manifesto.js` | Configurable rule engine with warn/fail thresholds; CI gate |
-| `audit.js` | Composite audit command: explain + impact + health in one call |
-| `batch.js` | Batch querying for multi-agent dispatch |
-| `triage.js` | Risk-ranked audit priority queue (delegates scoring to `graph/classifiers/`) |
-| `check.js` | CI validation predicates (cycles, complexity, blast radius, boundaries) |
-| `boundaries.js` | Architecture boundary rules with onion architecture preset |
-| `owners.js` | CODEOWNERS integration for ownership queries |
-| `snapshot.js` | SQLite DB backup and restore |
-| `sequence.js` | Sequence diagram data generation (BFS traversal); Mermaid rendering delegated to `presentation/sequence-renderer.js` |
 | `paginate.js` | Pagination helpers for bounded query results |
 | `logger.js` | Structured logging (`warn`, `debug`, `info`, `error`) |
+| **`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/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/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** |
+| `features/audit.js` | Composite audit command: explain + impact + health in one call |
+| `features/batch.js` | Batch querying for multi-agent dispatch |
+| `features/boundaries.js` | Architecture boundary rules with onion architecture preset |
+| `features/cfg.js` | Control-flow graph generation |
+| `features/check.js` | CI validation predicates (cycles, complexity, blast radius, boundaries) |
+| `features/communities.js` | Louvain community detection, drift analysis (delegates to `graph/` subsystem) |
+| `features/complexity.js` | Cognitive, cyclomatic, Halstead, MI computation from AST |
+| `features/dataflow.js` | Dataflow analysis |
+| `features/export.js` | Graph export orchestration: loads data from DB, delegates to `presentation/` serializers |
+| `features/manifesto.js` | Configurable rule engine with warn/fail thresholds; CI gate |
+| `features/owners.js` | CODEOWNERS integration for ownership queries |
+| `features/sequence.js` | Sequence diagram data generation (BFS traversal) |
+| `features/snapshot.js` | SQLite DB backup and restore |
+| `features/structure.js` | Codebase structure analysis |
+| `features/triage.js` | Risk-ranked audit priority queue (delegates scoring to `graph/classifiers/`) |
+| **`presentation/`** | **Pure output formatting** |
+| `presentation/` | `viewer.js` (HTML renderer), `export.js` (DOT/Mermaid/GraphML/Neo4j serializers), `sequence-renderer.js` (Mermaid sequence diagrams), `table.js` (CLI table formatting), `result-formatter.js` (JSON/NDJSON output) |
+| **`graph/`** | **Unified graph model** |
+| `graph/` | `CodeGraph` class (`model.js`), algorithms (Tarjan SCC, Louvain, BFS, shortest path, centrality), classifiers (role, risk), builders (dependency, structure, temporal) |
+| **`mcp/`** | **MCP server** |
+| `mcp/` | MCP server exposing graph queries to AI agents; single-repo by default, `--multi-repo` to enable cross-repo access |
+| `ast-analysis/` | Unified AST analysis framework: shared DFS walker (`visitor.js`), engine orchestrator (`engine.js`), extracted metrics (`metrics.js`), and pluggable visitors for complexity, dataflow, and AST-store |
 
 **Key design decisions:**
 - **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
-- **Node kinds:** `SYMBOL_KINDS` in `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`
+- **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
 - Import resolution uses a 6-level priority system with confidence scoring (import-aware → same-file → directory → parent → global → method hierarchy)

src/ast-analysis/engine.js

@@ -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/cli/commands/audit.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/batch.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/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]',

src/cli/commands/cfg.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/check.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/children.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/complexity.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/context.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>',

src/cli/commands/cycles.js

@@ -1,5 +1,5 @@
-import { findCycles, formatCycles } from '../../cycles.js';
-import { openReadonlyOrFail } from '../../db.js';
+import { openReadonlyOrFail } from '../../db/index.js';
+import { findCycles, formatCycles } from '../../domain/graph/cycles.js';
 
 export const command = {
   name: 'cycles',

src/cli/commands/dataflow.js

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

src/cli/commands/deps.js

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

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]',

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]',

src/cli/commands/export.js

@@ -1,13 +1,13 @@
 import fs from 'node:fs';
-import { openReadonlyOrFail } from '../../db.js';
+import { openReadonlyOrFail } from '../../db/index.js';
 import {
   exportDOT,
   exportGraphML,
   exportGraphSON,
   exportJSON,
   exportMermaid,
   exportNeo4jCSV,
-} from '../../export.js';
+} from '../../features/export.js';
 
 export const command = {
   name: 'export',

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>',

src/cli/commands/flow.js

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

src/cli/commands/fn-impact.js

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

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>',

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',

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',

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>',

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 { openReadonlyOrFail } from '../../db/index.js';
 
 export const command = {
   name: 'plot',

src/cli/commands/query.js

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

src/cli/commands/roles.js

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

src/cli/commands/search.js

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

src/cli/commands/sequence.js

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

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',

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',

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 { EVERY_SYMBOL_KIND, VALID_ROLES } from '../../queries.js';
 
 export const command = {
   name: 'triage',

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]',

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]',

src/commands/audit.js

@@ -1,6 +1,6 @@
-import { auditData } from '../audit.js';
+import { kindIcon } from '../domain/queries.js';
+import { auditData } from '../features/audit.js';
 import { outputResult } from '../infrastructure/result-formatter.js';
-import { kindIcon } from '../queries.js';
 
 /**
  * CLI formatter for the audit command.

src/commands/batch.js

@@ -1,4 +1,4 @@
-import { batchData, multiBatchData } from '../batch.js';
+import { batchData, multiBatchData } from '../features/batch.js';
 
 /**
  * CLI wrapper — calls batchData and prints JSON to stdout.

src/commands/branch-compare.js

@@ -1,6 +1,6 @@
-import { branchCompareData, branchCompareMermaid } from '../branch-compare.js';
+import { kindIcon } from '../domain/queries.js';
+import { branchCompareData, branchCompareMermaid } from '../features/branch-compare.js';
 import { outputResult } from '../infrastructure/result-formatter.js';
-import { kindIcon } from '../queries.js';
 
 // ─── Text Formatting ────────────────────────────────────────────────────
 

src/commands/cfg.js

@@ -1,4 +1,4 @@
-import { cfgData, cfgToDOT, cfgToMermaid } from '../cfg.js';
+import { cfgData, cfgToDOT, cfgToMermaid } from '../features/cfg.js';
 import { outputResult } from '../infrastructure/result-formatter.js';
 
 /**

src/commands/check.js

@@ -1,5 +1,5 @@
-import { checkData } from '../check.js';
 import { AnalysisError } from '../errors.js';
+import { checkData } from '../features/check.js';
 import { outputResult } from '../infrastructure/result-formatter.js';
 
 /**

src/commands/communities.js

@@ -1,4 +1,4 @@
-import { communitiesData } from '../communities.js';
+import { communitiesData } from '../features/communities.js';
 import { outputResult } from '../infrastructure/result-formatter.js';
 
 /**

src/commands/complexity.js

@@ -1,4 +1,4 @@
-import { complexityData } from '../complexity.js';
+import { complexityData } from '../features/complexity.js';
 import { outputResult } from '../infrastructure/result-formatter.js';
 
 /**

src/commands/dataflow.js

@@ -1,4 +1,4 @@
-import { dataflowData, dataflowImpactData } from '../dataflow.js';
+import { dataflowData, dataflowImpactData } from '../features/dataflow.js';
 import { outputResult } from '../infrastructure/result-formatter.js';
 
 /**

src/commands/flow.js

@@ -1,6 +1,6 @@
-import { flowData, listEntryPointsData } from '../flow.js';
+import { kindIcon } from '../domain/queries.js';
+import { flowData, listEntryPointsData } from '../features/flow.js';
 import { outputResult } from '../infrastructure/result-formatter.js';
-import { kindIcon } from '../queries.js';
 
 /**
  * CLI formatter — text or JSON output.

src/commands/manifesto.js

@@ -1,5 +1,5 @@
+import { manifestoData } from '../features/manifesto.js';
 import { outputResult } from '../infrastructure/result-formatter.js';
-import { manifestoData } from '../manifesto.js';
 
 /**
  * CLI formatter — prints manifesto results and sets exitCode 1 on failure.

src/commands/owners.js

@@ -1,5 +1,5 @@
+import { ownersData } from '../features/owners.js';
 import { outputResult } from '../infrastructure/result-formatter.js';
-import { ownersData } from '../owners.js';
 
 /**
  * CLI display function for the `owners` command.