diff --git a/CLAUDE.md b/CLAUDE.md
index bafb0d8b..efef122f 100644
--- a/CLAUDE.md
+++ b/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)
diff --git a/src/ast-analysis/engine.js b/src/ast-analysis/engine.js
index e45e1eb8..3998e313 100644
--- a/src/ast-analysis/engine.js
+++ b/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 {
diff --git a/src/cli/commands/audit.js b/src/cli/commands/audit.js
index 8a3de7cf..caa0b747 100644
--- a/src/cli/commands/audit.js
+++ b/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>',
diff --git a/src/cli/commands/batch.js b/src/cli/commands/batch.js
index 7637b5fb..8ba4f99c 100644
--- a/src/cli/commands/batch.js
+++ b/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...]',
diff --git a/src/cli/commands/build.js b/src/cli/commands/build.js
index 614d7098..f913945d 100644
--- a/src/cli/commands/build.js
+++ b/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]',
diff --git a/src/cli/commands/cfg.js b/src/cli/commands/cfg.js
index a6034e2e..20ef05bb 100644
--- a/src/cli/commands/cfg.js
+++ b/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>',
diff --git a/src/cli/commands/check.js b/src/cli/commands/check.js
index 78edb0b9..43d98a3a 100644
--- a/src/cli/commands/check.js
+++ b/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]',
diff --git a/src/cli/commands/children.js b/src/cli/commands/children.js
index 909c13d4..3412dcf4 100644
--- a/src/cli/commands/children.js
+++ b/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>',
diff --git a/src/cli/commands/complexity.js b/src/cli/commands/complexity.js
index 5211b197..193271d3 100644
--- a/src/cli/commands/complexity.js
+++ b/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]',
diff --git a/src/cli/commands/context.js b/src/cli/commands/context.js
index d2bbec9e..7a4e53da 100644
--- a/src/cli/commands/context.js
+++ b/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>',
diff --git a/src/cli/commands/cycles.js b/src/cli/commands/cycles.js
index e5f09dc4..614473af 100644
--- a/src/cli/commands/cycles.js
+++ b/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',
diff --git a/src/cli/commands/dataflow.js b/src/cli/commands/dataflow.js
index 2c6b57a9..4118b5b3 100644
--- a/src/cli/commands/dataflow.js
+++ b/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>',
diff --git a/src/cli/commands/deps.js b/src/cli/commands/deps.js
index 872f2888..a7644eff 100644
--- a/src/cli/commands/deps.js
+++ b/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>',
diff --git a/src/cli/commands/diff-impact.js b/src/cli/commands/diff-impact.js
index cf15f599..15fd67c9 100644
--- a/src/cli/commands/diff-impact.js
+++ b/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]',
diff --git a/src/cli/commands/embed.js b/src/cli/commands/embed.js
index 075520cd..c6bfb363 100644
--- a/src/cli/commands/embed.js
+++ b/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]',
diff --git a/src/cli/commands/export.js b/src/cli/commands/export.js
index 7bca538c..fd69c51a 100644
--- a/src/cli/commands/export.js
+++ b/src/cli/commands/export.js
@@ -1,5 +1,5 @@
 import fs from 'node:fs';
-import { openReadonlyOrFail } from '../../db.js';
+import { openReadonlyOrFail } from '../../db/index.js';
 import {
   exportDOT,
   exportGraphML,
@@ -7,7 +7,7 @@ import {
   exportJSON,
   exportMermaid,
   exportNeo4jCSV,
-} from '../../export.js';
+} from '../../features/export.js';
 
 export const command = {
   name: 'export',
diff --git a/src/cli/commands/exports.js b/src/cli/commands/exports.js
index a94c1c9f..2334f1ba 100644
--- a/src/cli/commands/exports.js
+++ b/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>',
diff --git a/src/cli/commands/flow.js b/src/cli/commands/flow.js
index 13332c23..20814a3c 100644
--- a/src/cli/commands/flow.js
+++ b/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]',
diff --git a/src/cli/commands/fn-impact.js b/src/cli/commands/fn-impact.js
index 50a8fbbe..5c64831f 100644
--- a/src/cli/commands/fn-impact.js
+++ b/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>',
diff --git a/src/cli/commands/impact.js b/src/cli/commands/impact.js
index a20e199e..fa4c5585 100644
--- a/src/cli/commands/impact.js
+++ b/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>',
diff --git a/src/cli/commands/map.js b/src/cli/commands/map.js
index ae5d8bff..370d2c25 100644
--- a/src/cli/commands/map.js
+++ b/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',
diff --git a/src/cli/commands/models.js b/src/cli/commands/models.js
index 0763650a..3ae9fc0f 100644
--- a/src/cli/commands/models.js
+++ b/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',
diff --git a/src/cli/commands/path.js b/src/cli/commands/path.js
index 44a20d14..34f53248 100644
--- a/src/cli/commands/path.js
+++ b/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>',
diff --git a/src/cli/commands/plot.js b/src/cli/commands/plot.js
index 9bc5925b..8dafe532 100644
--- a/src/cli/commands/plot.js
+++ b/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',
diff --git a/src/cli/commands/query.js b/src/cli/commands/query.js
index 2c4ee642..ac758116 100644
--- a/src/cli/commands/query.js
+++ b/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>',
diff --git a/src/cli/commands/roles.js b/src/cli/commands/roles.js
index 225c17bf..0380bee4 100644
--- a/src/cli/commands/roles.js
+++ b/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',
diff --git a/src/cli/commands/search.js b/src/cli/commands/search.js
index 238b59a0..e8670691 100644
--- a/src/cli/commands/search.js
+++ b/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>',
diff --git a/src/cli/commands/sequence.js b/src/cli/commands/sequence.js
index a07f784b..343a9fac 100644
--- a/src/cli/commands/sequence.js
+++ b/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>',
diff --git a/src/cli/commands/snapshot.js b/src/cli/commands/snapshot.js
index 8dd0093e..666f0f47 100644
--- a/src/cli/commands/snapshot.js
+++ b/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',
diff --git a/src/cli/commands/stats.js b/src/cli/commands/stats.js
index c0f6e2de..e9b4e9fa 100644
--- a/src/cli/commands/stats.js
+++ b/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',
diff --git a/src/cli/commands/triage.js b/src/cli/commands/triage.js
index a334475f..851df8e9 100644
--- a/src/cli/commands/triage.js
+++ b/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',
diff --git a/src/cli/commands/watch.js b/src/cli/commands/watch.js
index 78858158..8e55e2fc 100644
--- a/src/cli/commands/watch.js
+++ b/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]',
diff --git a/src/cli/commands/where.js b/src/cli/commands/where.js
index 382c1f21..9f0d37a9 100644
--- a/src/cli/commands/where.js
+++ b/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]',
diff --git a/src/commands/audit.js b/src/commands/audit.js
index 6cfeb3d7..13e4d488 100644
--- a/src/commands/audit.js
+++ b/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.
diff --git a/src/commands/batch.js b/src/commands/batch.js
index 60fdd3c1..bec40cf9 100644
--- a/src/commands/batch.js
+++ b/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.
diff --git a/src/commands/branch-compare.js b/src/commands/branch-compare.js
index aa1f2ef7..c90394fb 100644
--- a/src/commands/branch-compare.js
+++ b/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 ────────────────────────────────────────────────────
 
diff --git a/src/commands/cfg.js b/src/commands/cfg.js
index c0f6c13b..97b1e414 100644
--- a/src/commands/cfg.js
+++ b/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';
 
 /**
diff --git a/src/commands/check.js b/src/commands/check.js
index 114b09f6..eb592fe0 100644
--- a/src/commands/check.js
+++ b/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';
 
 /**
diff --git a/src/commands/communities.js b/src/commands/communities.js
index db21afba..ae1e8fb7 100644
--- a/src/commands/communities.js
+++ b/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';
 
 /**
diff --git a/src/commands/complexity.js b/src/commands/complexity.js
index 419064c2..f2de7f6a 100644
--- a/src/commands/complexity.js
+++ b/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';
 
 /**
diff --git a/src/commands/dataflow.js b/src/commands/dataflow.js
index 258f0d9c..fafcfb21 100644
--- a/src/commands/dataflow.js
+++ b/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';
 
 /**
diff --git a/src/commands/flow.js b/src/commands/flow.js
index 630bcff4..e86f2de9 100644
--- a/src/commands/flow.js
+++ b/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.
diff --git a/src/commands/manifesto.js b/src/commands/manifesto.js
index 0ccf1d1e..f491e0bf 100644
--- a/src/commands/manifesto.js
+++ b/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.
diff --git a/src/commands/owners.js b/src/commands/owners.js
index 3923cce0..2ec0f5c3 100644
--- a/src/commands/owners.js
+++ b/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.
diff --git a/src/commands/query.js b/src/commands/query.js
index 63c4db64..471e45c0 100644
--- a/src/commands/query.js
+++ b/src/commands/query.js
@@ -18,4 +18,4 @@ export {
   stats,
   symbolPath,
   where,
-} from '../queries-cli.js';
+} from '../presentation/queries-cli.js';
diff --git a/src/commands/sequence.js b/src/commands/sequence.js
index 3b0a2a9e..ff8946c0 100644
--- a/src/commands/sequence.js
+++ b/src/commands/sequence.js
@@ -1,6 +1,6 @@
+import { kindIcon } from '../domain/queries.js';
+import { sequenceData, sequenceToMermaid } from '../features/sequence.js';
 import { outputResult } from '../infrastructure/result-formatter.js';
-import { kindIcon } from '../queries.js';
-import { sequenceData, sequenceToMermaid } from '../sequence.js';
 
 /**
  * CLI entry point — format sequence data as mermaid, JSON, or ndjson.
diff --git a/src/commands/structure.js b/src/commands/structure.js
index b76df909..a2679a4f 100644
--- a/src/commands/structure.js
+++ b/src/commands/structure.js
@@ -1,5 +1,5 @@
 import path from 'node:path';
-import { hotspotsData, moduleBoundariesData, structureData } from '../structure.js';
+import { hotspotsData, moduleBoundariesData, structureData } from '../features/structure.js';
 
 export { hotspotsData, moduleBoundariesData, structureData };
 
diff --git a/src/commands/triage.js b/src/commands/triage.js
index 2ca8d136..8c10cb03 100644
--- a/src/commands/triage.js
+++ b/src/commands/triage.js
@@ -1,5 +1,5 @@
+import { triageData } from '../features/triage.js';
 import { outputResult } from '../infrastructure/result-formatter.js';
-import { triageData } from '../triage.js';
 
 /**
  * Print triage results to console.
diff --git a/src/db.js b/src/db/index.js
similarity index 90%
rename from src/db.js
rename to src/db/index.js
index 7b67a9cf..fc947b23 100644
--- a/src/db.js
+++ b/src/db/index.js
@@ -1,13 +1,13 @@
-// Barrel re-export — keeps all existing `import { ... } from './db.js'` working.
-export { closeDb, findDbPath, openDb, openReadonlyOrFail } from './db/connection.js';
-export { getBuildMeta, initSchema, MIGRATIONS, setBuildMeta } from './db/migrations.js';
+// Barrel re-export — keeps all existing `import { ... } from '…/db/index.js'` working.
+export { closeDb, findDbPath, openDb, openReadonlyOrFail } from './connection.js';
+export { getBuildMeta, initSchema, MIGRATIONS, setBuildMeta } from './migrations.js';
 export {
   fanInJoinSQL,
   fanOutJoinSQL,
   kindInClause,
   NodeQuery,
   testFilterSQL,
-} from './db/query-builder.js';
+} from './query-builder.js';
 export {
   bulkNodeIdsByFile,
   countCrossFileCallers,
@@ -60,4 +60,4 @@ export {
   Repository,
   SqliteRepository,
   upsertCoChangeMeta,
-} from './db/repository/index.js';
+} from './repository/index.js';
diff --git a/src/analysis/context.js b/src/domain/analysis/context.js
similarity index 97%
rename from src/analysis/context.js
rename to src/domain/analysis/context.js
index 8710ac90..803fcc99 100644
--- a/src/analysis/context.js
+++ b/src/domain/analysis/context.js
@@ -12,18 +12,18 @@ import {
   findNodesByFile,
   getComplexityForNode,
   openReadonlyOrFail,
-} from '../db.js';
-import { isTestFile } from '../infrastructure/test-filter.js';
-import { paginateResult } from '../paginate.js';
+} from '../../db/index.js';
+import { isTestFile } from '../../infrastructure/test-filter.js';
+import { paginateResult } from '../../paginate.js';
 import {
   createFileLinesReader,
   extractSignature,
   extractSummary,
   isFileLikeTarget,
   readSourceRange,
-} from '../shared/file-utils.js';
-import { resolveMethodViaHierarchy } from '../shared/hierarchy.js';
-import { normalizeSymbol } from '../shared/normalize.js';
+} from '../../shared/file-utils.js';
+import { resolveMethodViaHierarchy } from '../../shared/hierarchy.js';
+import { normalizeSymbol } from '../../shared/normalize.js';
 import { findMatchingNodes } from './symbol-lookup.js';
 
 function explainFileImpl(db, target, getFileLines) {
diff --git a/src/analysis/dependencies.js b/src/domain/analysis/dependencies.js
similarity index 97%
rename from src/analysis/dependencies.js
rename to src/domain/analysis/dependencies.js
index 5503570c..63778733 100644
--- a/src/analysis/dependencies.js
+++ b/src/domain/analysis/dependencies.js
@@ -6,11 +6,11 @@ import {
   findImportTargets,
   findNodesByFile,
   openReadonlyOrFail,
-} from '../db.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';
+} 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 { findMatchingNodes } from './symbol-lookup.js';
 
 export function fileDepsData(file, customDbPath, opts = {}) {
diff --git a/src/analysis/exports.js b/src/domain/analysis/exports.js
similarity index 93%
rename from src/analysis/exports.js
rename to src/domain/analysis/exports.js
index 2d2de439..6088656f 100644
--- a/src/analysis/exports.js
+++ b/src/domain/analysis/exports.js
@@ -5,10 +5,14 @@ import {
   findFileNodes,
   findNodesByFile,
   openReadonlyOrFail,
-} from '../db.js';
-import { isTestFile } from '../infrastructure/test-filter.js';
-import { paginateResult } from '../paginate.js';
-import { createFileLinesReader, extractSignature, extractSummary } from '../shared/file-utils.js';
+} 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';
 
 export function exportsData(file, customDbPath, opts = {}) {
   const db = openReadonlyOrFail(customDbPath);
diff --git a/src/analysis/impact.js b/src/domain/analysis/impact.js
similarity index 96%
rename from src/analysis/impact.js
rename to src/domain/analysis/impact.js
index b4e18979..282e9c64 100644
--- a/src/analysis/impact.js
+++ b/src/domain/analysis/impact.js
@@ -1,9 +1,7 @@
 import { execFileSync } from 'node:child_process';
 import fs from 'node:fs';
 import path from 'node:path';
-import { evaluateBoundaries } from '../boundaries.js';
-import { coChangeForFiles } from '../cochange.js';
-import { loadConfig } from '../config.js';
+import { loadConfig } from '../../config.js';
 import {
   findDbPath,
   findDistinctCallers,
@@ -11,11 +9,13 @@ import {
   findImportDependents,
   findNodeById,
   openReadonlyOrFail,
-} from '../db.js';
-import { isTestFile } from '../infrastructure/test-filter.js';
-import { ownersForFiles } from '../owners.js';
-import { paginateResult } from '../paginate.js';
-import { normalizeSymbol } from '../shared/normalize.js';
+} from '../../db/index.js';
+import { evaluateBoundaries } from '../../features/boundaries.js';
+import { coChangeForFiles } from '../../features/cochange.js';
+import { ownersForFiles } from '../../features/owners.js';
+import { isTestFile } from '../../infrastructure/test-filter.js';
+import { paginateResult } from '../../paginate.js';
+import { normalizeSymbol } from '../../shared/normalize.js';
 import { findMatchingNodes } from './symbol-lookup.js';
 
 export function impactAnalysisData(file, customDbPath, opts = {}) {
diff --git a/src/analysis/module-map.js b/src/domain/analysis/module-map.js
similarity index 97%
rename from src/analysis/module-map.js
rename to src/domain/analysis/module-map.js
index 7c0bbcdb..fedef93e 100644
--- a/src/analysis/module-map.js
+++ b/src/domain/analysis/module-map.js
@@ -1,8 +1,8 @@
 import path from 'node:path';
-import { findCycles } from '../cycles.js';
-import { openReadonlyOrFail, testFilterSQL } from '../db.js';
-import { isTestFile } from '../infrastructure/test-filter.js';
-import { LANGUAGE_REGISTRY } from '../parser.js';
+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';
 
 export const FALSE_POSITIVE_NAMES = new Set([
   'run',
diff --git a/src/analysis/roles.js b/src/domain/analysis/roles.js
similarity index 83%
rename from src/analysis/roles.js
rename to src/domain/analysis/roles.js
index 5d76af95..d295515f 100644
--- a/src/analysis/roles.js
+++ b/src/domain/analysis/roles.js
@@ -1,7 +1,7 @@
-import { openReadonlyOrFail } from '../db.js';
-import { isTestFile } from '../infrastructure/test-filter.js';
-import { paginateResult } from '../paginate.js';
-import { normalizeSymbol } from '../shared/normalize.js';
+import { openReadonlyOrFail } from '../../db/index.js';
+import { isTestFile } from '../../infrastructure/test-filter.js';
+import { paginateResult } from '../../paginate.js';
+import { normalizeSymbol } from '../../shared/normalize.js';
 
 export function rolesData(customDbPath, opts = {}) {
   const db = openReadonlyOrFail(customDbPath);
diff --git a/src/analysis/symbol-lookup.js b/src/domain/analysis/symbol-lookup.js
similarity index 96%
rename from src/analysis/symbol-lookup.js
rename to src/domain/analysis/symbol-lookup.js
index 78ea24f6..e269a42d 100644
--- a/src/analysis/symbol-lookup.js
+++ b/src/domain/analysis/symbol-lookup.js
@@ -12,11 +12,11 @@ import {
   findNodesWithFanIn,
   listFunctionNodes,
   openReadonlyOrFail,
-} from '../db.js';
-import { isTestFile } from '../infrastructure/test-filter.js';
-import { ALL_SYMBOL_KINDS } from '../kinds.js';
-import { paginateResult } from '../paginate.js';
-import { getFileHash, normalizeSymbol } from '../shared/normalize.js';
+} from '../../db/index.js';
+import { isTestFile } from '../../infrastructure/test-filter.js';
+import { ALL_SYMBOL_KINDS } from '../../kinds.js';
+import { paginateResult } from '../../paginate.js';
+import { getFileHash, normalizeSymbol } from '../../shared/normalize.js';
 
 const FUNCTION_KINDS = ['function', 'method', 'class'];
 
diff --git a/src/builder.js b/src/domain/graph/builder.js
similarity index 100%
rename from src/builder.js
rename to src/domain/graph/builder.js
diff --git a/src/builder/context.js b/src/domain/graph/builder/context.js
similarity index 100%
rename from src/builder/context.js
rename to src/domain/graph/builder/context.js
diff --git a/src/builder/helpers.js b/src/domain/graph/builder/helpers.js
similarity index 97%
rename from src/builder/helpers.js
rename to src/domain/graph/builder/helpers.js
index 0ad89def..a333f456 100644
--- a/src/builder/helpers.js
+++ b/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.js';
-import { warn } from '../logger.js';
+import { EXTENSIONS, IGNORE_DIRS } from '../../../constants.js';
+import { purgeFilesData } from '../../../db/index.js';
+import { warn } from '../../../logger.js';
 
 export const BUILTIN_RECEIVERS = new Set([
   'console',
diff --git a/src/builder/incremental.js b/src/domain/graph/builder/incremental.js
similarity index 97%
rename from src/builder/incremental.js
rename to src/domain/graph/builder/incremental.js
index d30c89df..7183d4b7 100644
--- a/src/builder/incremental.js
+++ b/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 { normalizePath } from '../../../constants.js';
+import { warn } from '../../../logger.js';
+import { parseFileIncremental } from '../../../parser.js';
 import { computeConfidence, resolveImportPath } from '../resolve.js';
 import { BUILTIN_RECEIVERS, readFileSafe } from './helpers.js';
 
diff --git a/src/builder/pipeline.js b/src/domain/graph/builder/pipeline.js
similarity index 96%
rename from src/builder/pipeline.js
rename to src/domain/graph/builder/pipeline.js
index 09a97a5c..d1be7ebb 100644
--- a/src/builder/pipeline.js
+++ b/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.js';
-import { info } from '../logger.js';
-import { getActiveEngine } from '../parser.js';
+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 { PipelineContext } from './context.js';
 import { loadPathAliases } from './helpers.js';
 import { buildEdges } from './stages/build-edges.js';
diff --git a/src/builder/stages/build-edges.js b/src/domain/graph/builder/stages/build-edges.js
similarity index 99%
rename from src/builder/stages/build-edges.js
rename to src/domain/graph/builder/stages/build-edges.js
index 545aa9bf..33aa66ca 100644
--- a/src/builder/stages/build-edges.js
+++ b/src/domain/graph/builder/stages/build-edges.js
@@ -6,8 +6,8 @@
  */
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
-import { getNodeId } from '../../db.js';
-import { loadNative } from '../../native.js';
+import { getNodeId } from '../../../../db/index.js';
+import { loadNative } from '../../../../native.js';
 import { computeConfidence } from '../../resolve.js';
 import { BUILTIN_RECEIVERS, batchInsertEdges } from '../helpers.js';
 import { getResolved, isBarrelFile, resolveBarrelExport } from './resolve-imports.js';
diff --git a/src/builder/stages/build-structure.js b/src/domain/graph/builder/stages/build-structure.js
similarity index 94%
rename from src/builder/stages/build-structure.js
rename to src/domain/graph/builder/stages/build-structure.js
index 9f69e455..ec235be2 100644
--- a/src/builder/stages/build-structure.js
+++ b/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 { normalizePath } from '../../../../constants.js';
+import { debug } from '../../../../logger.js';
 import { readFileSafe } from '../helpers.js';
 
 /**
@@ -88,7 +88,7 @@ export async function buildStructure(ctx) {
     relDirs.add(normalizePath(path.relative(rootDir, absDir)));
   }
   try {
-    const { buildStructure: buildStructureFn } = await import('../../structure.js');
+    const { buildStructure: buildStructureFn } = await import('../../../../features/structure.js');
     const changedFilePaths = isFullBuild ? null : [...allSymbols.keys()];
     buildStructureFn(db, fileSymbols, rootDir, ctx.lineCountMap, relDirs, changedFilePaths);
   } catch (err) {
@@ -99,7 +99,7 @@ export async function buildStructure(ctx) {
   // Classify node roles
   const t1 = performance.now();
   try {
-    const { classifyNodeRoles } = await import('../../structure.js');
+    const { classifyNodeRoles } = await import('../../../../features/structure.js');
     const roleSummary = classifyNodeRoles(db);
     debug(
       `Roles: ${Object.entries(roleSummary)
diff --git a/src/builder/stages/collect-files.js b/src/domain/graph/builder/stages/collect-files.js
similarity index 92%
rename from src/builder/stages/collect-files.js
rename to src/domain/graph/builder/stages/collect-files.js
index 29511d21..97d183ce 100644
--- a/src/builder/stages/collect-files.js
+++ b/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 { normalizePath } from '../../../../constants.js';
+import { info } from '../../../../logger.js';
 import { collectFiles as collectFilesUtil } from '../helpers.js';
 
 /**
diff --git a/src/builder/stages/detect-changes.js b/src/domain/graph/builder/stages/detect-changes.js
similarity index 96%
rename from src/builder/stages/detect-changes.js
rename to src/domain/graph/builder/stages/detect-changes.js
index ce902a71..29d25a8a 100644
--- a/src/builder/stages/detect-changes.js
+++ b/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.js';
-import { readJournal, writeJournalHeader } from '../../journal.js';
-import { debug, info } from '../../logger.js';
-import { parseFilesAuto } from '../../parser.js';
+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 { fileHash, fileStat, purgeFilesFromGraph, readFileSafe } from '../helpers.js';
 
 /**
@@ -203,11 +203,11 @@ async function runPendingAnalysis(ctx) {
   };
   const analysisSymbols = await parseFilesAuto(allFiles, rootDir, analysisOpts);
   if (needsCfg) {
-    const { buildCFGData } = await import('../../cfg.js');
+    const { buildCFGData } = await import('../../../../features/cfg.js');
     await buildCFGData(db, analysisSymbols, rootDir, engineOpts);
   }
   if (needsDataflow) {
-    const { buildDataflowEdges } = await import('../../dataflow.js');
+    const { buildDataflowEdges } = await import('../../../../features/dataflow.js');
     await buildDataflowEdges(db, analysisSymbols, rootDir, engineOpts);
   }
   return true;
diff --git a/src/builder/stages/finalize.js b/src/domain/graph/builder/stages/finalize.js
similarity index 92%
rename from src/builder/stages/finalize.js
rename to src/domain/graph/builder/stages/finalize.js
index 1b59cebc..e82411d7 100644
--- a/src/builder/stages/finalize.js
+++ b/src/domain/graph/builder/stages/finalize.js
@@ -6,13 +6,13 @@
 import fs from 'node:fs';
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
-import { closeDb, getBuildMeta, setBuildMeta } from '../../db.js';
-import { writeJournalHeader } from '../../journal.js';
-import { debug, info, warn } from '../../logger.js';
+import { closeDb, getBuildMeta, setBuildMeta } from '../../../../db/index.js';
+import { writeJournalHeader } from '../../../../journal.js';
+import { debug, info, warn } from '../../../../logger.js';
 
 const __builderDir = path.dirname(new URL(import.meta.url).pathname.replace(/^\/([A-Z]:)/i, '$1'));
 const CODEGRAPH_VERSION = JSON.parse(
-  fs.readFileSync(path.join(__builderDir, '..', '..', '..', 'package.json'), 'utf-8'),
+  fs.readFileSync(path.join(__builderDir, '..', '..', '..', '..', '..', 'package.json'), 'utf-8'),
 ).version;
 
 /**
@@ -127,7 +127,7 @@ export async function finalize(ctx) {
       debug(`Skipping auto-registration for temp directory: ${resolvedRoot}`);
     } else {
       try {
-        const { registerRepo } = await import('../../registry.js');
+        const { registerRepo } = await import('../../../../registry.js');
         registerRepo(rootDir);
       } catch (err) {
         debug(`Auto-registration failed: ${err.message}`);
diff --git a/src/builder/stages/insert-nodes.js b/src/domain/graph/builder/stages/insert-nodes.js
similarity index 99%
rename from src/builder/stages/insert-nodes.js
rename to src/domain/graph/builder/stages/insert-nodes.js
index d0244268..2eaf6a73 100644
--- a/src/builder/stages/insert-nodes.js
+++ b/src/domain/graph/builder/stages/insert-nodes.js
@@ -6,7 +6,7 @@
  */
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
-import { bulkNodeIdsByFile } from '../../db.js';
+import { bulkNodeIdsByFile } from '../../../../db/index.js';
 import {
   batchInsertEdges,
   batchInsertNodes,
diff --git a/src/builder/stages/parse-files.js b/src/domain/graph/builder/stages/parse-files.js
similarity index 89%
rename from src/builder/stages/parse-files.js
rename to src/domain/graph/builder/stages/parse-files.js
index 3cdae46e..0d3e1167 100644
--- a/src/builder/stages/parse-files.js
+++ b/src/domain/graph/builder/stages/parse-files.js
@@ -5,8 +5,8 @@
  * Populates ctx.allSymbols, ctx.fileSymbols, ctx.filesToParse.
  */
 import { performance } from 'node:perf_hooks';
-import { info } from '../../logger.js';
-import { parseFilesAuto } from '../../parser.js';
+import { info } from '../../../../logger.js';
+import { parseFilesAuto } from '../../../../parser.js';
 
 /**
  * @param {import('../context.js').PipelineContext} ctx
diff --git a/src/builder/stages/resolve-imports.js b/src/domain/graph/builder/stages/resolve-imports.js
similarity index 98%
rename from src/builder/stages/resolve-imports.js
rename to src/domain/graph/builder/stages/resolve-imports.js
index 1fba3f53..d2a39861 100644
--- a/src/builder/stages/resolve-imports.js
+++ b/src/domain/graph/builder/stages/resolve-imports.js
@@ -6,7 +6,7 @@
  */
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
-import { parseFilesAuto } from '../../parser.js';
+import { parseFilesAuto } from '../../../../parser.js';
 import { resolveImportPath, resolveImportsBatch } from '../../resolve.js';
 
 /**
diff --git a/src/builder/stages/run-analyses.js b/src/domain/graph/builder/stages/run-analyses.js
similarity index 91%
rename from src/builder/stages/run-analyses.js
rename to src/domain/graph/builder/stages/run-analyses.js
index bc8db8a3..f6dbbdb9 100644
--- a/src/builder/stages/run-analyses.js
+++ b/src/domain/graph/builder/stages/run-analyses.js
@@ -4,7 +4,7 @@
  * Dispatches to the unified AST analysis engine (AST nodes, complexity, CFG, dataflow).
  * Filters out reverse-dep files for incremental builds.
  */
-import { debug, warn } from '../../logger.js';
+import { debug, warn } from '../../../../logger.js';
 
 /**
  * @param {import('../context.js').PipelineContext} ctx
@@ -31,7 +31,7 @@ export async function runAnalyses(ctx) {
     }
   }
 
-  const { runAnalyses: runAnalysesFn } = await import('../../ast-analysis/engine.js');
+  const { runAnalyses: runAnalysesFn } = await import('../../../../ast-analysis/engine.js');
   try {
     const analysisTiming = await runAnalysesFn(db, astComplexitySymbols, rootDir, opts, engineOpts);
     ctx.timing.astMs = analysisTiming.astMs;
diff --git a/src/cycles.js b/src/domain/graph/cycles.js
similarity index 91%
rename from src/cycles.js
rename to src/domain/graph/cycles.js
index a66b6ff0..bed9fc03 100644
--- a/src/cycles.js
+++ b/src/domain/graph/cycles.js
@@ -1,7 +1,7 @@
-import { tarjan } from './graph/algorithms/tarjan.js';
-import { buildDependencyGraph } from './graph/builders/dependency.js';
-import { CodeGraph } from './graph/model.js';
-import { loadNative } from './native.js';
+import { tarjan } from '../../graph/algorithms/tarjan.js';
+import { buildDependencyGraph } from '../../graph/builders/dependency.js';
+import { CodeGraph } from '../../graph/model.js';
+import { loadNative } from '../../native.js';
 
 /**
  * Detect circular dependencies in the codebase using Tarjan's SCC algorithm.
diff --git a/src/resolve.js b/src/domain/graph/resolve.js
similarity index 98%
rename from src/resolve.js
rename to src/domain/graph/resolve.js
index 8581b58c..73179b67 100644
--- a/src/resolve.js
+++ b/src/domain/graph/resolve.js
@@ -1,7 +1,7 @@
 import fs from 'node:fs';
 import path from 'node:path';
-import { normalizePath } from './constants.js';
-import { loadNative } from './native.js';
+import { normalizePath } from '../../constants.js';
+import { loadNative } from '../../native.js';
 
 // ── Alias format conversion ─────────────────────────────────────────
 
diff --git a/src/watcher.js b/src/domain/graph/watcher.js
similarity index 93%
rename from src/watcher.js
rename to src/domain/graph/watcher.js
index 8c5ed85b..58b56eeb 100644
--- a/src/watcher.js
+++ b/src/domain/graph/watcher.js
@@ -1,13 +1,13 @@
 import fs from 'node:fs';
 import path from 'node:path';
+import { appendChangeEvents, buildChangeEvent, diffSymbols } from '../../change-journal.js';
+import { EXTENSIONS, IGNORE_DIRS, normalizePath } from '../../constants.js';
+import { closeDb, getNodeId as getNodeIdQuery, initSchema, openDb } from '../../db/index.js';
+import { DbError } from '../../errors.js';
+import { appendJournalEntries } from '../../journal.js';
+import { info } from '../../logger.js';
+import { createParseTreeCache, getActiveEngine } from '../../parser.js';
 import { rebuildFile } from './builder/incremental.js';
-import { appendChangeEvents, buildChangeEvent, diffSymbols } from './change-journal.js';
-import { EXTENSIONS, IGNORE_DIRS, normalizePath } from './constants.js';
-import { closeDb, getNodeId as getNodeIdQuery, initSchema, openDb } from './db.js';
-import { DbError } from './errors.js';
-import { appendJournalEntries } from './journal.js';
-import { info } from './logger.js';
-import { createParseTreeCache, getActiveEngine } from './parser.js';
 
 function shouldIgnore(filePath) {
   const parts = filePath.split(path.sep);
diff --git a/src/queries.js b/src/domain/queries.js
similarity index 87%
rename from src/queries.js
rename to src/domain/queries.js
index 68121023..4b853d79 100644
--- a/src/queries.js
+++ b/src/domain/queries.js
@@ -6,6 +6,22 @@
  * importers continue to work without changes.
  */
 
+// ── Re-export from dedicated module for backward compat ───────────────────
+export { isTestFile, TEST_PATTERN } from '../infrastructure/test-filter.js';
+// ── Kind/edge constants (canonical source: kinds.js) ─────────────────────
+export {
+  ALL_SYMBOL_KINDS,
+  CORE_EDGE_KINDS,
+  CORE_SYMBOL_KINDS,
+  EVERY_EDGE_KIND,
+  EVERY_SYMBOL_KIND,
+  EXTENDED_SYMBOL_KINDS,
+  STRUCTURAL_EDGE_KINDS,
+  VALID_ROLES,
+} from '../kinds.js';
+export { iterListFunctions, iterRoles, iterWhere } from '../shared/generators.js';
+// ── Shared utilities ─────────────────────────────────────────────────────
+export { kindIcon, normalizeSymbol } from '../shared/normalize.js';
 export { contextData, explainData } from './analysis/context.js';
 export { fileDepsData, fnDepsData, pathData } from './analysis/dependencies.js';
 export { exportsData } from './analysis/exports.js';
@@ -30,19 +46,3 @@ export {
   queryNameData,
   whereData,
 } from './analysis/symbol-lookup.js';
-// ── Re-export from dedicated module for backward compat ───────────────────
-export { isTestFile, TEST_PATTERN } from './infrastructure/test-filter.js';
-// ── Kind/edge constants (canonical source: kinds.js) ─────────────────────
-export {
-  ALL_SYMBOL_KINDS,
-  CORE_EDGE_KINDS,
-  CORE_SYMBOL_KINDS,
-  EVERY_EDGE_KIND,
-  EVERY_SYMBOL_KIND,
-  EXTENDED_SYMBOL_KINDS,
-  STRUCTURAL_EDGE_KINDS,
-  VALID_ROLES,
-} from './kinds.js';
-export { iterListFunctions, iterRoles, iterWhere } from './shared/generators.js';
-// ── Shared utilities ─────────────────────────────────────────────────────
-export { kindIcon, normalizeSymbol } from './shared/normalize.js';
diff --git a/src/embeddings/generator.js b/src/domain/search/generator.js
similarity index 97%
rename from src/embeddings/generator.js
rename to src/domain/search/generator.js
index b34f5934..6936dd84 100644
--- a/src/embeddings/generator.js
+++ b/src/domain/search/generator.js
@@ -1,8 +1,8 @@
 import fs from 'node:fs';
 import path from 'node:path';
-import { closeDb, findDbPath, openDb } from '../db.js';
-import { DbError } from '../errors.js';
-import { warn } from '../logger.js';
+import { closeDb, findDbPath, openDb } from '../../db/index.js';
+import { DbError } from '../../errors.js';
+import { warn } from '../../logger.js';
 import { embed, getModelConfig } from './models.js';
 import { buildSourceText } from './strategies/source.js';
 import { buildStructuredText } from './strategies/structured.js';
diff --git a/src/embeddings/index.js b/src/domain/search/index.js
similarity index 100%
rename from src/embeddings/index.js
rename to src/domain/search/index.js
diff --git a/src/embeddings/models.js b/src/domain/search/models.js
similarity index 98%
rename from src/embeddings/models.js
rename to src/domain/search/models.js
index 1202dd28..355dd381 100644
--- a/src/embeddings/models.js
+++ b/src/domain/search/models.js
@@ -1,7 +1,7 @@
 import { execFileSync } from 'node:child_process';
 import { createInterface } from 'node:readline';
-import { ConfigError, EngineError } from '../errors.js';
-import { info } from '../logger.js';
+import { ConfigError, EngineError } from '../../errors.js';
+import { info } from '../../logger.js';
 
 // Lazy-load transformers (heavy, optional module)
 let pipeline = null;
diff --git a/src/embeddings/search/cli-formatter.js b/src/domain/search/search/cli-formatter.js
similarity index 99%
rename from src/embeddings/search/cli-formatter.js
rename to src/domain/search/search/cli-formatter.js
index f79a9e27..013333af 100644
--- a/src/embeddings/search/cli-formatter.js
+++ b/src/domain/search/search/cli-formatter.js
@@ -1,4 +1,4 @@
-import { warn } from '../../logger.js';
+import { warn } from '../../../logger.js';
 import { hybridSearchData } from './hybrid.js';
 import { ftsSearchData } from './keyword.js';
 import { multiSearchData, searchData } from './semantic.js';
diff --git a/src/embeddings/search/filters.js b/src/domain/search/search/filters.js
similarity index 100%
rename from src/embeddings/search/filters.js
rename to src/domain/search/search/filters.js
diff --git a/src/embeddings/search/hybrid.js b/src/domain/search/search/hybrid.js
similarity index 98%
rename from src/embeddings/search/hybrid.js
rename to src/domain/search/search/hybrid.js
index 759e91c7..6d236568 100644
--- a/src/embeddings/search/hybrid.js
+++ b/src/domain/search/search/hybrid.js
@@ -1,4 +1,4 @@
-import { openReadonlyOrFail } from '../../db.js';
+import { openReadonlyOrFail } from '../../../db/index.js';
 import { hasFtsIndex } from '../stores/fts5.js';
 import { ftsSearchData } from './keyword.js';
 import { searchData } from './semantic.js';
diff --git a/src/embeddings/search/keyword.js b/src/domain/search/search/keyword.js
similarity index 96%
rename from src/embeddings/search/keyword.js
rename to src/domain/search/search/keyword.js
index cc8975d3..e43c5212 100644
--- a/src/embeddings/search/keyword.js
+++ b/src/domain/search/search/keyword.js
@@ -1,4 +1,4 @@
-import { openReadonlyOrFail } from '../../db.js';
+import { openReadonlyOrFail } from '../../../db/index.js';
 import { normalizeSymbol } from '../../queries.js';
 import { hasFtsIndex, sanitizeFtsQuery } from '../stores/fts5.js';
 import { applyFilters } from './filters.js';
diff --git a/src/embeddings/search/prepare.js b/src/domain/search/search/prepare.js
similarity index 93%
rename from src/embeddings/search/prepare.js
rename to src/domain/search/search/prepare.js
index 864bfbe9..484584c5 100644
--- a/src/embeddings/search/prepare.js
+++ b/src/domain/search/search/prepare.js
@@ -1,5 +1,5 @@
-import { getEmbeddingCount, getEmbeddingMeta } from '../../db/repository/embeddings.js';
-import { openReadonlyOrFail } from '../../db.js';
+import { openReadonlyOrFail } from '../../../db/index.js';
+import { getEmbeddingCount, getEmbeddingMeta } from '../../../db/repository/embeddings.js';
 import { MODELS } from '../models.js';
 import { applyFilters } from './filters.js';
 
diff --git a/src/embeddings/search/semantic.js b/src/domain/search/search/semantic.js
similarity index 99%
rename from src/embeddings/search/semantic.js
rename to src/domain/search/search/semantic.js
index 62263ac3..aa624ab6 100644
--- a/src/embeddings/search/semantic.js
+++ b/src/domain/search/search/semantic.js
@@ -1,4 +1,4 @@
-import { warn } from '../../logger.js';
+import { warn } from '../../../logger.js';
 import { normalizeSymbol } from '../../queries.js';
 import { embed } from '../models.js';
 import { cosineSim } from '../stores/sqlite-blob.js';
diff --git a/src/embeddings/stores/fts5.js b/src/domain/search/stores/fts5.js
similarity index 100%
rename from src/embeddings/stores/fts5.js
rename to src/domain/search/stores/fts5.js
diff --git a/src/embeddings/stores/sqlite-blob.js b/src/domain/search/stores/sqlite-blob.js
similarity index 100%
rename from src/embeddings/stores/sqlite-blob.js
rename to src/domain/search/stores/sqlite-blob.js
diff --git a/src/embeddings/strategies/source.js b/src/domain/search/strategies/source.js
similarity index 100%
rename from src/embeddings/strategies/source.js
rename to src/domain/search/strategies/source.js
diff --git a/src/embeddings/strategies/structured.js b/src/domain/search/strategies/structured.js
similarity index 95%
rename from src/embeddings/strategies/structured.js
rename to src/domain/search/strategies/structured.js
index c488d1c6..83f5ff0a 100644
--- a/src/embeddings/strategies/structured.js
+++ b/src/domain/search/strategies/structured.js
@@ -1,4 +1,4 @@
-import { findCalleeNames, findCallerNames } from '../../db.js';
+import { findCalleeNames, findCallerNames } from '../../../db/index.js';
 import { extractLeadingComment, splitIdentifier } from './text-utils.js';
 
 /**
diff --git a/src/embeddings/strategies/text-utils.js b/src/domain/search/strategies/text-utils.js
similarity index 100%
rename from src/embeddings/strategies/text-utils.js
rename to src/domain/search/strategies/text-utils.js
diff --git a/src/ast.js b/src/features/ast.js
similarity index 94%
rename from src/ast.js
rename to src/features/ast.js
index b0ad6d72..6935efe7 100644
--- a/src/ast.js
+++ b/src/features/ast.js
@@ -7,14 +7,14 @@
  */
 
 import path from 'node:path';
-import { AST_TYPE_MAPS } from './ast-analysis/rules/index.js';
-import { buildExtensionSet } from './ast-analysis/shared.js';
-import { walkWithVisitors } from './ast-analysis/visitor.js';
-import { createAstStoreVisitor } from './ast-analysis/visitors/ast-store-visitor.js';
-import { bulkNodeIdsByFile, openReadonlyOrFail } from './db.js';
-import { outputResult } from './infrastructure/result-formatter.js';
-import { debug } from './logger.js';
-import { paginateResult } from './paginate.js';
+import { AST_TYPE_MAPS } from '../ast-analysis/rules/index.js';
+import { buildExtensionSet } from '../ast-analysis/shared.js';
+import { walkWithVisitors } from '../ast-analysis/visitor.js';
+import { createAstStoreVisitor } from '../ast-analysis/visitors/ast-store-visitor.js';
+import { bulkNodeIdsByFile, openReadonlyOrFail } from '../db/index.js';
+import { outputResult } from '../infrastructure/result-formatter.js';
+import { debug } from '../logger.js';
+import { paginateResult } from '../paginate.js';
 
 // ─── Constants ────────────────────────────────────────────────────────
 
diff --git a/src/audit.js b/src/features/audit.js
similarity index 98%
rename from src/audit.js
rename to src/features/audit.js
index 63e5c08b..c267b04a 100644
--- a/src/audit.js
+++ b/src/features/audit.js
@@ -7,11 +7,11 @@
  */
 
 import path from 'node:path';
-import { loadConfig } from './config.js';
-import { openReadonlyOrFail } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
+import { loadConfig } from '../config.js';
+import { openReadonlyOrFail } from '../db/index.js';
+import { explainData } from '../domain/queries.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
 import { RULE_DEFS } from './manifesto.js';
-import { explainData } from './queries.js';
 
 // ─── Threshold resolution ───────────────────────────────────────────
 
diff --git a/src/batch.js b/src/features/batch.js
similarity index 98%
rename from src/batch.js
rename to src/features/batch.js
index fb4ce88d..4d1225bd 100644
--- a/src/batch.js
+++ b/src/features/batch.js
@@ -5,10 +5,6 @@
  * Designed for multi-agent swarms that need to dispatch 20+ queries in one call.
  */
 
-import { complexityData } from './complexity.js';
-import { dataflowData } from './dataflow.js';
-import { ConfigError } from './errors.js';
-import { flowData } from './flow.js';
 import {
   contextData,
   explainData,
@@ -18,7 +14,11 @@ import {
   fnImpactData,
   impactAnalysisData,
   whereData,
-} from './queries.js';
+} from '../domain/queries.js';
+import { ConfigError } from '../errors.js';
+import { complexityData } from './complexity.js';
+import { dataflowData } from './dataflow.js';
+import { flowData } from './flow.js';
 
 /**
  * Map of supported batch commands → their data function + first-arg semantics.
diff --git a/src/boundaries.js b/src/features/boundaries.js
similarity index 99%
rename from src/boundaries.js
rename to src/features/boundaries.js
index 6bf92fd4..8da92b92 100644
--- a/src/boundaries.js
+++ b/src/features/boundaries.js
@@ -1,5 +1,5 @@
-import { isTestFile } from './infrastructure/test-filter.js';
-import { debug } from './logger.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { debug } from '../logger.js';
 
 // ─── Glob-to-Regex ───────────────────────────────────────────────────
 
diff --git a/src/branch-compare.js b/src/features/branch-compare.js
similarity index 98%
rename from src/branch-compare.js
rename to src/features/branch-compare.js
index 29172c7e..474e162e 100644
--- a/src/branch-compare.js
+++ b/src/features/branch-compare.js
@@ -11,9 +11,9 @@ import fs from 'node:fs';
 import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
-import { buildGraph } from './builder.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { kindIcon } from './queries.js';
+import { buildGraph } from '../domain/graph/builder.js';
+import { kindIcon } from '../domain/queries.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
 
 // ─── Git Helpers ────────────────────────────────────────────────────────
 
diff --git a/src/cfg.js b/src/features/cfg.js
similarity index 97%
rename from src/cfg.js
rename to src/features/cfg.js
index cf023f3b..6f1dcdfc 100644
--- a/src/cfg.js
+++ b/src/features/cfg.js
@@ -7,14 +7,14 @@
 
 import fs from 'node:fs';
 import path from 'node:path';
-import { CFG_RULES } from './ast-analysis/rules/index.js';
+import { CFG_RULES } from '../ast-analysis/rules/index.js';
 import {
   makeCfgRules as _makeCfgRules,
   buildExtensionSet,
   buildExtToLangMap,
-} from './ast-analysis/shared.js';
-import { walkWithVisitors } from './ast-analysis/visitor.js';
-import { createCfgVisitor } from './ast-analysis/visitors/cfg-visitor.js';
+} from '../ast-analysis/shared.js';
+import { walkWithVisitors } from '../ast-analysis/visitor.js';
+import { createCfgVisitor } from '../ast-analysis/visitors/cfg-visitor.js';
 import {
   deleteCfgForNode,
   getCfgBlocks,
@@ -22,10 +22,10 @@ import {
   getFunctionNodeId,
   hasCfgTables,
   openReadonlyOrFail,
-} from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { info } from './logger.js';
-import { paginateResult } from './paginate.js';
+} from '../db/index.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { info } from '../logger.js';
+import { paginateResult } from '../paginate.js';
 
 // Re-export for backward compatibility
 export { _makeCfgRules as makeCfgRules, CFG_RULES };
diff --git a/src/check.js b/src/features/check.js
similarity index 98%
rename from src/check.js
rename to src/features/check.js
index dd53de50..b8e3c75f 100644
--- a/src/check.js
+++ b/src/features/check.js
@@ -1,10 +1,10 @@
 import { execFileSync } from 'node:child_process';
 import fs from 'node:fs';
 import path from 'node:path';
-import { loadConfig } from './config.js';
-import { findCycles } from './cycles.js';
-import { findDbPath, openReadonlyOrFail } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
+import { loadConfig } from '../config.js';
+import { findDbPath, openReadonlyOrFail } from '../db/index.js';
+import { findCycles } from '../domain/graph/cycles.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
 import { matchOwners, parseCodeowners } from './owners.js';
 
 // ─── Diff Parser ──────────────────────────────────────────────────────
diff --git a/src/cochange.js b/src/features/cochange.js
similarity index 98%
rename from src/cochange.js
rename to src/features/cochange.js
index 182e4d9e..134519ed 100644
--- a/src/cochange.js
+++ b/src/features/cochange.js
@@ -8,11 +8,11 @@
 import { execFileSync } from 'node:child_process';
 import fs from 'node:fs';
 import path from 'node:path';
-import { normalizePath } from './constants.js';
-import { closeDb, findDbPath, initSchema, openDb, openReadonlyOrFail } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { warn } from './logger.js';
-import { paginateResult } from './paginate.js';
+import { normalizePath } from '../constants.js';
+import { closeDb, findDbPath, initSchema, openDb, openReadonlyOrFail } from '../db/index.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { warn } from '../logger.js';
+import { paginateResult } from '../paginate.js';
 
 /**
  * Scan git history and return parsed commit data.
diff --git a/src/communities.js b/src/features/communities.js
similarity index 95%
rename from src/communities.js
rename to src/features/communities.js
index e0d51ae2..51970558 100644
--- a/src/communities.js
+++ b/src/features/communities.js
@@ -1,8 +1,8 @@
 import path from 'node:path';
-import { openReadonlyOrFail } from './db.js';
-import { louvainCommunities } from './graph/algorithms/louvain.js';
-import { buildDependencyGraph } from './graph/builders/dependency.js';
-import { paginateResult } from './paginate.js';
+import { openReadonlyOrFail } from '../db/index.js';
+import { louvainCommunities } from '../graph/algorithms/louvain.js';
+import { buildDependencyGraph } from '../graph/builders/dependency.js';
+import { paginateResult } from '../paginate.js';
 
 // ─── Directory Helpers ────────────────────────────────────────────────
 
diff --git a/src/complexity.js b/src/features/complexity.js
similarity index 97%
rename from src/complexity.js
rename to src/features/complexity.js
index fce3d89b..b319c945 100644
--- a/src/complexity.js
+++ b/src/features/complexity.js
@@ -3,20 +3,20 @@ import path from 'node:path';
 import {
   computeLOCMetrics as _computeLOCMetrics,
   computeMaintainabilityIndex as _computeMaintainabilityIndex,
-} from './ast-analysis/metrics.js';
-import { COMPLEXITY_RULES, HALSTEAD_RULES } from './ast-analysis/rules/index.js';
+} from '../ast-analysis/metrics.js';
+import { COMPLEXITY_RULES, HALSTEAD_RULES } from '../ast-analysis/rules/index.js';
 import {
   findFunctionNode as _findFunctionNode,
   buildExtensionSet,
   buildExtToLangMap,
-} from './ast-analysis/shared.js';
-import { walkWithVisitors } from './ast-analysis/visitor.js';
-import { createComplexityVisitor } from './ast-analysis/visitors/complexity-visitor.js';
-import { loadConfig } from './config.js';
-import { getFunctionNodeId, openReadonlyOrFail } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { info } from './logger.js';
-import { paginateResult } from './paginate.js';
+} from '../ast-analysis/shared.js';
+import { walkWithVisitors } from '../ast-analysis/visitor.js';
+import { createComplexityVisitor } from '../ast-analysis/visitors/complexity-visitor.js';
+import { loadConfig } from '../config.js';
+import { getFunctionNodeId, openReadonlyOrFail } from '../db/index.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { info } from '../logger.js';
+import { paginateResult } from '../paginate.js';
 
 // Re-export rules for backward compatibility
 export { COMPLEXITY_RULES, HALSTEAD_RULES };
diff --git a/src/dataflow.js b/src/features/dataflow.js
similarity index 97%
rename from src/dataflow.js
rename to src/features/dataflow.js
index 5ed355e1..dbff4cda 100644
--- a/src/dataflow.js
+++ b/src/features/dataflow.js
@@ -11,19 +11,19 @@
 
 import fs from 'node:fs';
 import path from 'node:path';
-import { DATAFLOW_RULES } from './ast-analysis/rules/index.js';
+import { DATAFLOW_RULES } from '../ast-analysis/rules/index.js';
 import {
   makeDataflowRules as _makeDataflowRules,
   buildExtensionSet,
   buildExtToLangMap,
-} from './ast-analysis/shared.js';
-import { walkWithVisitors } from './ast-analysis/visitor.js';
-import { createDataflowVisitor } from './ast-analysis/visitors/dataflow-visitor.js';
-import { hasDataflowTable, openReadonlyOrFail } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { info } from './logger.js';
-import { paginateResult } from './paginate.js';
-import { ALL_SYMBOL_KINDS, normalizeSymbol } from './queries.js';
+} from '../ast-analysis/shared.js';
+import { walkWithVisitors } from '../ast-analysis/visitor.js';
+import { createDataflowVisitor } from '../ast-analysis/visitors/dataflow-visitor.js';
+import { hasDataflowTable, openReadonlyOrFail } from '../db/index.js';
+import { ALL_SYMBOL_KINDS, normalizeSymbol } from '../domain/queries.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { info } from '../logger.js';
+import { paginateResult } from '../paginate.js';
 
 // Re-export for backward compatibility
 export { _makeDataflowRules as makeDataflowRules, DATAFLOW_RULES };
diff --git a/src/export.js b/src/features/export.js
similarity index 98%
rename from src/export.js
rename to src/features/export.js
index 8dfa768b..61ed15ba 100644
--- a/src/export.js
+++ b/src/features/export.js
@@ -1,6 +1,6 @@
 import path from 'node:path';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { paginateResult } from './paginate.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { paginateResult } from '../paginate.js';
 import {
   renderFileLevelDOT,
   renderFileLevelGraphML,
@@ -10,7 +10,7 @@ import {
   renderFunctionLevelGraphML,
   renderFunctionLevelMermaid,
   renderFunctionLevelNeo4jCSV,
-} from './presentation/export.js';
+} from '../presentation/export.js';
 
 const DEFAULT_MIN_CONFIDENCE = 0.5;
 
diff --git a/src/flow.js b/src/features/flow.js
similarity index 96%
rename from src/flow.js
rename to src/features/flow.js
index e3af32bd..8f42af3a 100644
--- a/src/flow.js
+++ b/src/features/flow.js
@@ -5,10 +5,10 @@
  * framework entry points (routes, commands, events) through their call chains.
  */
 
-import { openReadonlyOrFail } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { paginateResult } from './paginate.js';
-import { CORE_SYMBOL_KINDS, findMatchingNodes } from './queries.js';
+import { openReadonlyOrFail } from '../db/index.js';
+import { CORE_SYMBOL_KINDS, findMatchingNodes } from '../domain/queries.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { paginateResult } from '../paginate.js';
 import { FRAMEWORK_ENTRY_PREFIXES } from './structure.js';
 
 /**
diff --git a/src/manifesto.js b/src/features/manifesto.js
similarity index 98%
rename from src/manifesto.js
rename to src/features/manifesto.js
index 234391fd..c77ae21d 100644
--- a/src/manifesto.js
+++ b/src/features/manifesto.js
@@ -1,9 +1,9 @@
+import { loadConfig } from '../config.js';
+import { openReadonlyOrFail } from '../db/index.js';
+import { findCycles } from '../domain/graph/cycles.js';
+import { debug } from '../logger.js';
+import { paginateResult } from '../paginate.js';
 import { evaluateBoundaries } from './boundaries.js';
-import { loadConfig } from './config.js';
-import { findCycles } from './cycles.js';
-import { openReadonlyOrFail } from './db.js';
-import { debug } from './logger.js';
-import { paginateResult } from './paginate.js';
 
 // ─── Rule Definitions ─────────────────────────────────────────────────
 
diff --git a/src/owners.js b/src/features/owners.js
similarity index 98%
rename from src/owners.js
rename to src/features/owners.js
index e0fef2e3..58509ff9 100644
--- a/src/owners.js
+++ b/src/features/owners.js
@@ -1,7 +1,7 @@
 import fs from 'node:fs';
 import path from 'node:path';
-import { findDbPath, openReadonlyOrFail } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
+import { findDbPath, openReadonlyOrFail } from '../db/index.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
 
 // ─── CODEOWNERS Parsing ──────────────────────────────────────────────
 
diff --git a/src/sequence.js b/src/features/sequence.js
similarity index 96%
rename from src/sequence.js
rename to src/features/sequence.js
index 5d87a1f0..78a3d68a 100644
--- a/src/sequence.js
+++ b/src/features/sequence.js
@@ -6,10 +6,10 @@
  * sequence-diagram conventions.
  */
 
-import { findCallees, openReadonlyOrFail } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { paginateResult } from './paginate.js';
-import { findMatchingNodes } from './queries.js';
+import { findCallees, openReadonlyOrFail } from '../db/index.js';
+import { findMatchingNodes } from '../domain/queries.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { paginateResult } from '../paginate.js';
 import { FRAMEWORK_ENTRY_PREFIXES } from './structure.js';
 
 // ─── Alias generation ────────────────────────────────────────────────
@@ -286,4 +286,4 @@ export function sequenceData(name, dbPath, opts = {}) {
 }
 
 // Re-export Mermaid renderer from presentation layer
-export { sequenceToMermaid } from './presentation/sequence-renderer.js';
+export { sequenceToMermaid } from '../presentation/sequence-renderer.js';
diff --git a/src/snapshot.js b/src/features/snapshot.js
similarity index 96%
rename from src/snapshot.js
rename to src/features/snapshot.js
index 0ce12bf5..007549aa 100644
--- a/src/snapshot.js
+++ b/src/features/snapshot.js
@@ -1,9 +1,9 @@
 import fs from 'node:fs';
 import path from 'node:path';
 import Database from 'better-sqlite3';
-import { findDbPath } from './db.js';
-import { ConfigError, DbError } from './errors.js';
-import { debug } from './logger.js';
+import { findDbPath } from '../db/index.js';
+import { ConfigError, DbError } from '../errors.js';
+import { debug } from '../logger.js';
 
 const NAME_RE = /^[a-zA-Z0-9_-]+$/;
 
diff --git a/src/structure.js b/src/features/structure.js
similarity index 98%
rename from src/structure.js
rename to src/features/structure.js
index 8a65125e..7fcd5628 100644
--- a/src/structure.js
+++ b/src/features/structure.js
@@ -1,9 +1,9 @@
 import path from 'node:path';
-import { normalizePath } from './constants.js';
-import { getNodeId, openReadonlyOrFail, testFilterSQL } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { debug } from './logger.js';
-import { paginateResult } from './paginate.js';
+import { normalizePath } from '../constants.js';
+import { getNodeId, openReadonlyOrFail, testFilterSQL } from '../db/index.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { debug } from '../logger.js';
+import { paginateResult } from '../paginate.js';
 
 // ─── Build-time: insert directory nodes, contains edges, and metrics ────
 
@@ -313,9 +313,9 @@ export function buildStructure(db, fileSymbols, _rootDir, lineCountMap, director
 // ─── Node role classification ─────────────────────────────────────────
 
 // Re-export from classifier for backward compatibility
-export { FRAMEWORK_ENTRY_PREFIXES } from './graph/classifiers/roles.js';
+export { FRAMEWORK_ENTRY_PREFIXES } from '../graph/classifiers/roles.js';
 
-import { classifyRoles } from './graph/classifiers/roles.js';
+import { classifyRoles } from '../graph/classifiers/roles.js';
 
 export function classifyNodeRoles(db) {
   const rows = db
diff --git a/src/triage.js b/src/features/triage.js
similarity index 93%
rename from src/triage.js
rename to src/features/triage.js
index 5f02aa9e..5cd9d7a1 100644
--- a/src/triage.js
+++ b/src/features/triage.js
@@ -1,8 +1,8 @@
-import { findNodesForTriage, openReadonlyOrFail } from './db.js';
-import { DEFAULT_WEIGHTS, scoreRisk } from './graph/classifiers/risk.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { warn } from './logger.js';
-import { paginateResult } from './paginate.js';
+import { findNodesForTriage, openReadonlyOrFail } from '../db/index.js';
+import { DEFAULT_WEIGHTS, scoreRisk } from '../graph/classifiers/risk.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { warn } from '../logger.js';
+import { paginateResult } from '../paginate.js';
 
 // ─── Data Function ────────────────────────────────────────────────────
 
diff --git a/src/viewer.js b/src/features/viewer.js
similarity index 96%
rename from src/viewer.js
rename to src/features/viewer.js
index fb438823..96e47e2c 100644
--- a/src/viewer.js
+++ b/src/features/viewer.js
@@ -1,16 +1,16 @@
 import path from 'node:path';
-import { louvainCommunities } from './graph/algorithms/louvain.js';
-import { CodeGraph } from './graph/model.js';
-import { isTestFile } from './infrastructure/test-filter.js';
+import { louvainCommunities } from '../graph/algorithms/louvain.js';
+import { CodeGraph } from '../graph/model.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
 import {
   COMMUNITY_COLORS,
   DEFAULT_NODE_COLORS,
   DEFAULT_ROLE_COLORS,
-} from './presentation/colors.js';
-import { DEFAULT_CONFIG, renderPlotHTML } from './presentation/viewer.js';
+} from '../presentation/colors.js';
+import { DEFAULT_CONFIG, renderPlotHTML } from '../presentation/viewer.js';
 
 // Re-export presentation utilities for backward compatibility
-export { loadPlotConfig } from './presentation/viewer.js';
+export { loadPlotConfig } from '../presentation/viewer.js';
 
 const DEFAULT_MIN_CONFIDENCE = 0.5;
 
diff --git a/src/graph/builders/dependency.js b/src/graph/builders/dependency.js
index b0e24f78..a494ef11 100644
--- a/src/graph/builders/dependency.js
+++ b/src/graph/builders/dependency.js
@@ -3,7 +3,7 @@
  * Replaces inline graph construction in cycles.js, communities.js, viewer.js, export.js.
  */
 
-import { getCallableNodes, getCallEdges, getFileNodesAll, getImportEdges } from '../../db.js';
+import { getCallableNodes, getCallEdges, getFileNodesAll, getImportEdges } from '../../db/index.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
 import { CodeGraph } from '../model.js';
 
diff --git a/src/index.js b/src/index.js
index 576efac6..a50e9017 100644
--- a/src/index.js
+++ b/src/index.js
@@ -9,41 +9,10 @@
  *   import { buildGraph, queryNameData, findCycles, exportDOT } from '@optave/codegraph';
  */
 
-export { astQueryData } from './ast.js';
-export { auditData } from './audit.js';
-export { batchData } from './batch.js';
-export { branchCompareData } from './branch-compare.js';
-export { buildGraph } from './builder.js';
-export { cfgData } from './cfg.js';
-export { checkData } from './check.js';
-export { coChangeData } from './cochange.js';
-export { communitiesData } from './communities.js';
-export { complexityData } from './complexity.js';
 export { loadConfig } from './config.js';
 export { EXTENSIONS, IGNORE_DIRS } from './constants.js';
-export { findCycles } from './cycles.js';
-export { dataflowData } from './dataflow.js';
-export {
-  buildEmbeddings,
-  hybridSearchData,
-  multiSearchData,
-  searchData,
-} from './embeddings/index.js';
-export {
-  AnalysisError,
-  BoundaryError,
-  CodegraphError,
-  ConfigError,
-  DbError,
-  EngineError,
-  ParseError,
-  ResolutionError,
-} from './errors.js';
-export { exportDOT, exportJSON, exportMermaid } from './export.js';
-export { flowData, listEntryPointsData } from './flow.js';
-export { EVERY_EDGE_KIND, EVERY_SYMBOL_KIND } from './kinds.js';
-export { manifestoData } from './manifesto.js';
-export { ownersData } from './owners.js';
+export { buildGraph } from './domain/graph/builder.js';
+export { findCycles } from './domain/graph/cycles.js';
 export {
   childrenData,
   contextData,
@@ -60,7 +29,38 @@ export {
   rolesData,
   statsData,
   whereData,
-} from './queries.js';
-export { sequenceData } from './sequence.js';
-export { hotspotsData, moduleBoundariesData, structureData } from './structure.js';
-export { triageData } from './triage.js';
+} from './domain/queries.js';
+export {
+  buildEmbeddings,
+  hybridSearchData,
+  multiSearchData,
+  searchData,
+} from './domain/search/index.js';
+export {
+  AnalysisError,
+  BoundaryError,
+  CodegraphError,
+  ConfigError,
+  DbError,
+  EngineError,
+  ParseError,
+  ResolutionError,
+} from './errors.js';
+export { astQueryData } from './features/ast.js';
+export { auditData } from './features/audit.js';
+export { batchData } from './features/batch.js';
+export { branchCompareData } from './features/branch-compare.js';
+export { cfgData } from './features/cfg.js';
+export { checkData } from './features/check.js';
+export { coChangeData } from './features/cochange.js';
+export { communitiesData } from './features/communities.js';
+export { complexityData } from './features/complexity.js';
+export { dataflowData } from './features/dataflow.js';
+export { exportDOT, exportJSON, exportMermaid } from './features/export.js';
+export { flowData, listEntryPointsData } from './features/flow.js';
+export { manifestoData } from './features/manifesto.js';
+export { ownersData } from './features/owners.js';
+export { sequenceData } from './features/sequence.js';
+export { hotspotsData, moduleBoundariesData, structureData } from './features/structure.js';
+export { triageData } from './features/triage.js';
+export { EVERY_EDGE_KIND, EVERY_SYMBOL_KIND } from './kinds.js';
diff --git a/src/mcp.js b/src/mcp.js
deleted file mode 100644
index 51d59cd9..00000000
--- a/src/mcp.js
+++ /dev/null
@@ -1,2 +0,0 @@
-export { startMCPServer } from './mcp/server.js';
-export { buildToolList, TOOLS } from './mcp/tool-registry.js';
diff --git a/src/mcp/server.js b/src/mcp/server.js
index 3a39aed8..b5c1ea92 100644
--- a/src/mcp/server.js
+++ b/src/mcp/server.js
@@ -6,7 +6,7 @@
  */
 
 import { createRequire } from 'node:module';
-import { findDbPath } from '../db.js';
+import { findDbPath } from '../db/index.js';
 import { CodegraphError, ConfigError } from '../errors.js';
 import { MCP_MAX_LIMIT } from '../paginate.js';
 import { buildToolList } from './tool-registry.js';
@@ -48,7 +48,7 @@ export async function startMCPServer(customDbPath, options = {}) {
 
   async function getQueries() {
     if (!_queries) {
-      _queries = await import('../queries.js');
+      _queries = await import('../domain/queries.js');
     }
     return _queries;
   }
diff --git a/src/mcp/tool-registry.js b/src/mcp/tool-registry.js
index 7247b271..a09beea1 100644
--- a/src/mcp/tool-registry.js
+++ b/src/mcp/tool-registry.js
@@ -4,8 +4,8 @@
  * Owns BASE_TOOLS, LIST_REPOS_TOOL, buildToolList(), and the backward-compatible TOOLS export.
  */
 
-import { AST_NODE_KINDS } from '../ast.js';
-import { EVERY_EDGE_KIND, EVERY_SYMBOL_KIND, VALID_ROLES } from '../queries.js';
+import { EVERY_EDGE_KIND, EVERY_SYMBOL_KIND, VALID_ROLES } from '../domain/queries.js';
+import { AST_NODE_KINDS } from '../features/ast.js';
 
 const REPO_PROP = {
   repo: {
diff --git a/src/mcp/tools/ast-query.js b/src/mcp/tools/ast-query.js
index 97a5b124..a353e7ea 100644
--- a/src/mcp/tools/ast-query.js
+++ b/src/mcp/tools/ast-query.js
@@ -3,7 +3,7 @@ import { effectiveLimit, effectiveOffset } from '../middleware.js';
 export const name = 'ast_query';
 
 export async function handler(args, ctx) {
-  const { astQueryData } = await import('../../ast.js');
+  const { astQueryData } = await import('../../features/ast.js');
   return astQueryData(args.pattern, ctx.dbPath, {
     kind: args.kind,
     file: args.file,
diff --git a/src/mcp/tools/audit.js b/src/mcp/tools/audit.js
index 7dd47b43..c4438ba1 100644
--- a/src/mcp/tools/audit.js
+++ b/src/mcp/tools/audit.js
@@ -11,7 +11,7 @@ export async function handler(args, ctx) {
       offset: effectiveOffset(args),
     });
   }
-  const { auditData } = await import('../../audit.js');
+  const { auditData } = await import('../../features/audit.js');
   return auditData(args.target, ctx.dbPath, {
     depth: args.depth,
     file: args.file,
diff --git a/src/mcp/tools/batch-query.js b/src/mcp/tools/batch-query.js
index f93f979b..01dc19ba 100644
--- a/src/mcp/tools/batch-query.js
+++ b/src/mcp/tools/batch-query.js
@@ -1,7 +1,7 @@
 export const name = 'batch_query';
 
 export async function handler(args, ctx) {
-  const { batchData } = await import('../../batch.js');
+  const { batchData } = await import('../../features/batch.js');
   return batchData(args.command, args.targets, ctx.dbPath, {
     depth: args.depth,
     file: args.file,
diff --git a/src/mcp/tools/branch-compare.js b/src/mcp/tools/branch-compare.js
index 21e363c8..a01022dd 100644
--- a/src/mcp/tools/branch-compare.js
+++ b/src/mcp/tools/branch-compare.js
@@ -1,7 +1,9 @@
 export const name = 'branch_compare';
 
 export async function handler(args, _ctx) {
-  const { branchCompareData, branchCompareMermaid } = await import('../../branch-compare.js');
+  const { branchCompareData, branchCompareMermaid } = await import(
+    '../../features/branch-compare.js'
+  );
   const bcData = await branchCompareData(args.base, args.target, {
     depth: args.depth,
     noTests: args.no_tests,
diff --git a/src/mcp/tools/cfg.js b/src/mcp/tools/cfg.js
index 07524cf7..bb77c455 100644
--- a/src/mcp/tools/cfg.js
+++ b/src/mcp/tools/cfg.js
@@ -3,7 +3,7 @@ import { effectiveOffset, MCP_DEFAULTS } from '../middleware.js';
 export const name = 'cfg';
 
 export async function handler(args, ctx) {
-  const { cfgData, cfgToDOT, cfgToMermaid } = await import('../../cfg.js');
+  const { cfgData, cfgToDOT, cfgToMermaid } = await import('../../features/cfg.js');
   const cfgResult = cfgData(args.name, ctx.dbPath, {
     file: args.file,
     kind: args.kind,
diff --git a/src/mcp/tools/check.js b/src/mcp/tools/check.js
index 48c57e7a..e1e587c6 100644
--- a/src/mcp/tools/check.js
+++ b/src/mcp/tools/check.js
@@ -6,7 +6,7 @@ export async function handler(args, ctx) {
   const isDiffMode = args.ref || args.staged;
 
   if (!isDiffMode && !args.rules) {
-    const { manifestoData } = await import('../../manifesto.js');
+    const { manifestoData } = await import('../../features/manifesto.js');
     return manifestoData(ctx.dbPath, {
       file: args.file,
       noTests: args.no_tests,
@@ -16,7 +16,7 @@ export async function handler(args, ctx) {
     });
   }
 
-  const { checkData } = await import('../../check.js');
+  const { checkData } = await import('../../features/check.js');
   const checkResult = checkData(ctx.dbPath, {
     ref: args.ref,
     staged: args.staged,
@@ -29,7 +29,7 @@ export async function handler(args, ctx) {
   });
 
   if (args.rules) {
-    const { manifestoData } = await import('../../manifesto.js');
+    const { manifestoData } = await import('../../features/manifesto.js');
     const manifestoResult = manifestoData(ctx.dbPath, {
       file: args.file,
       noTests: args.no_tests,
diff --git a/src/mcp/tools/co-changes.js b/src/mcp/tools/co-changes.js
index 5e6fcab0..32efa4ac 100644
--- a/src/mcp/tools/co-changes.js
+++ b/src/mcp/tools/co-changes.js
@@ -3,7 +3,7 @@ import { effectiveLimit, effectiveOffset } from '../middleware.js';
 export const name = 'co_changes';
 
 export async function handler(args, ctx) {
-  const { coChangeData, coChangeTopData } = await import('../../cochange.js');
+  const { coChangeData, coChangeTopData } = await import('../../features/cochange.js');
   return args.file
     ? coChangeData(args.file, ctx.dbPath, {
         limit: effectiveLimit(args, name),
diff --git a/src/mcp/tools/code-owners.js b/src/mcp/tools/code-owners.js
index 633cc58c..7fe97d7d 100644
--- a/src/mcp/tools/code-owners.js
+++ b/src/mcp/tools/code-owners.js
@@ -1,7 +1,7 @@
 export const name = 'code_owners';
 
 export async function handler(args, ctx) {
-  const { ownersData } = await import('../../owners.js');
+  const { ownersData } = await import('../../features/owners.js');
   return ownersData(ctx.dbPath, {
     file: args.file,
     owner: args.owner,
diff --git a/src/mcp/tools/communities.js b/src/mcp/tools/communities.js
index 0c491976..1ec66a0b 100644
--- a/src/mcp/tools/communities.js
+++ b/src/mcp/tools/communities.js
@@ -3,7 +3,7 @@ import { effectiveLimit, effectiveOffset } from '../middleware.js';
 export const name = 'communities';
 
 export async function handler(args, ctx) {
-  const { communitiesData } = await import('../../communities.js');
+  const { communitiesData } = await import('../../features/communities.js');
   return communitiesData(ctx.dbPath, {
     functions: args.functions,
     resolution: args.resolution,
diff --git a/src/mcp/tools/complexity.js b/src/mcp/tools/complexity.js
index c5639cb1..3c999773 100644
--- a/src/mcp/tools/complexity.js
+++ b/src/mcp/tools/complexity.js
@@ -3,7 +3,7 @@ import { effectiveLimit, effectiveOffset } from '../middleware.js';
 export const name = 'complexity';
 
 export async function handler(args, ctx) {
-  const { complexityData } = await import('../../complexity.js');
+  const { complexityData } = await import('../../features/complexity.js');
   return complexityData(ctx.dbPath, {
     target: args.name,
     file: args.file,
diff --git a/src/mcp/tools/dataflow.js b/src/mcp/tools/dataflow.js
index a3e19198..39d84db9 100644
--- a/src/mcp/tools/dataflow.js
+++ b/src/mcp/tools/dataflow.js
@@ -5,7 +5,7 @@ export const name = 'dataflow';
 export async function handler(args, ctx) {
   const dfMode = args.mode || 'edges';
   if (dfMode === 'impact') {
-    const { dataflowImpactData } = await import('../../dataflow.js');
+    const { dataflowImpactData } = await import('../../features/dataflow.js');
     return dataflowImpactData(args.name, ctx.dbPath, {
       depth: args.depth,
       file: args.file,
@@ -15,7 +15,7 @@ export async function handler(args, ctx) {
       offset: effectiveOffset(args),
     });
   }
-  const { dataflowData } = await import('../../dataflow.js');
+  const { dataflowData } = await import('../../features/dataflow.js');
   return dataflowData(args.name, ctx.dbPath, {
     file: args.file,
     kind: args.kind,
diff --git a/src/mcp/tools/execution-flow.js b/src/mcp/tools/execution-flow.js
index e2932000..d8fefb1c 100644
--- a/src/mcp/tools/execution-flow.js
+++ b/src/mcp/tools/execution-flow.js
@@ -4,7 +4,7 @@ export const name = 'execution_flow';
 
 export async function handler(args, ctx) {
   if (args.list) {
-    const { listEntryPointsData } = await import('../../flow.js');
+    const { listEntryPointsData } = await import('../../features/flow.js');
     return listEntryPointsData(ctx.dbPath, {
       noTests: args.no_tests,
       limit: effectiveLimit(args, name),
@@ -14,7 +14,7 @@ export async function handler(args, ctx) {
   if (!args.name) {
     return { error: 'Provide a name or set list=true' };
   }
-  const { flowData } = await import('../../flow.js');
+  const { flowData } = await import('../../features/flow.js');
   return flowData(args.name, ctx.dbPath, {
     depth: args.depth,
     file: args.file,
diff --git a/src/mcp/tools/export-graph.js b/src/mcp/tools/export-graph.js
index 900abb36..e632086f 100644
--- a/src/mcp/tools/export-graph.js
+++ b/src/mcp/tools/export-graph.js
@@ -1,11 +1,11 @@
-import { findDbPath } from '../../db.js';
+import { findDbPath } from '../../db/index.js';
 import { effectiveOffset, MCP_DEFAULTS, MCP_MAX_LIMIT } from '../middleware.js';
 
 export const name = 'export_graph';
 
 export async function handler(args, ctx) {
   const { exportDOT, exportGraphML, exportGraphSON, exportJSON, exportMermaid, exportNeo4jCSV } =
-    await import('../../export.js');
+    await import('../../features/export.js');
   const Database = ctx.getDatabase();
   const db = new Database(findDbPath(ctx.dbPath), { readonly: true });
   const fileLevel = args.file_level !== false;
diff --git a/src/mcp/tools/find-cycles.js b/src/mcp/tools/find-cycles.js
index df366101..6a24f581 100644
--- a/src/mcp/tools/find-cycles.js
+++ b/src/mcp/tools/find-cycles.js
@@ -1,5 +1,5 @@
-import { findCycles } from '../../cycles.js';
-import { findDbPath } from '../../db.js';
+import { findDbPath } from '../../db/index.js';
+import { findCycles } from '../../domain/graph/cycles.js';
 
 export const name = 'find_cycles';
 
diff --git a/src/mcp/tools/sequence.js b/src/mcp/tools/sequence.js
index 4712e015..8209cb36 100644
--- a/src/mcp/tools/sequence.js
+++ b/src/mcp/tools/sequence.js
@@ -3,7 +3,7 @@ import { effectiveOffset, MCP_DEFAULTS } from '../middleware.js';
 export const name = 'sequence';
 
 export async function handler(args, ctx) {
-  const { sequenceData, sequenceToMermaid } = await import('../../sequence.js');
+  const { sequenceData, sequenceToMermaid } = await import('../../features/sequence.js');
   const seqResult = sequenceData(args.name, ctx.dbPath, {
     depth: args.depth,
     file: args.file,
diff --git a/src/mcp/tools/structure.js b/src/mcp/tools/structure.js
index 27aba582..51dc453f 100644
--- a/src/mcp/tools/structure.js
+++ b/src/mcp/tools/structure.js
@@ -3,7 +3,7 @@ import { effectiveLimit, effectiveOffset } from '../middleware.js';
 export const name = 'structure';
 
 export async function handler(args, ctx) {
-  const { structureData } = await import('../../structure.js');
+  const { structureData } = await import('../../features/structure.js');
   return structureData(ctx.dbPath, {
     directory: args.directory,
     depth: args.depth,
diff --git a/src/mcp/tools/triage.js b/src/mcp/tools/triage.js
index 2d84efa6..b153a76b 100644
--- a/src/mcp/tools/triage.js
+++ b/src/mcp/tools/triage.js
@@ -4,7 +4,7 @@ export const name = 'triage';
 
 export async function handler(args, ctx) {
   if (args.level === 'file' || args.level === 'directory') {
-    const { hotspotsData } = await import('../../structure.js');
+    const { hotspotsData } = await import('../../features/structure.js');
     const TRIAGE_TO_HOTSPOT = {
       risk: 'fan-in',
       complexity: 'density',
@@ -20,7 +20,7 @@ export async function handler(args, ctx) {
       noTests: args.no_tests,
     });
   }
-  const { triageData } = await import('../../triage.js');
+  const { triageData } = await import('../../features/triage.js');
   return triageData(ctx.dbPath, {
     sort: args.sort,
     minScore: args.min_score,
diff --git a/src/queries-cli.js b/src/presentation/queries-cli.js
similarity index 99%
rename from src/queries-cli.js
rename to src/presentation/queries-cli.js
index f4981a31..8eab363e 100644
--- a/src/queries-cli.js
+++ b/src/presentation/queries-cli.js
@@ -7,7 +7,6 @@
  */
 
 import path from 'node:path';
-import { outputResult } from './infrastructure/result-formatter.js';
 import {
   childrenData,
   contextData,
@@ -26,7 +25,8 @@ import {
   rolesData,
   statsData,
   whereData,
-} from './queries.js';
+} from '../domain/queries.js';
+import { outputResult } from '../infrastructure/result-formatter.js';
 
 // ─── symbolPath ─────────────────────────────────────────────────────────
 
diff --git a/src/shared/generators.js b/src/shared/generators.js
index 56c58b0d..93753dbd 100644
--- a/src/shared/generators.js
+++ b/src/shared/generators.js
@@ -1,4 +1,4 @@
-import { iterateFunctionNodes, openReadonlyOrFail } from '../db.js';
+import { iterateFunctionNodes, openReadonlyOrFail } from '../db/index.js';
 import { isTestFile } from '../infrastructure/test-filter.js';
 import { ALL_SYMBOL_KINDS } from '../kinds.js';
 
diff --git a/src/shared/hierarchy.js b/src/shared/hierarchy.js
index 7be0eaf3..d2d511fc 100644
--- a/src/shared/hierarchy.js
+++ b/src/shared/hierarchy.js
@@ -1,4 +1,4 @@
-import { getClassHierarchy } from '../db.js';
+import { getClassHierarchy } from '../db/index.js';
 
 export function resolveMethodViaHierarchy(db, methodName) {
   const methods = db
diff --git a/tests/builder/collect-files.test.js b/tests/builder/collect-files.test.js
index 709ef352..4d4955c5 100644
--- a/tests/builder/collect-files.test.js
+++ b/tests/builder/collect-files.test.js
@@ -5,8 +5,8 @@ import fs from 'node:fs';
 import os from 'node:os';
 import path from 'node:path';
 import { afterAll, beforeAll, describe, expect, it } from 'vitest';
-import { PipelineContext } from '../../src/builder/context.js';
-import { collectFiles } from '../../src/builder/stages/collect-files.js';
+import { PipelineContext } from '../../src/domain/graph/builder/context.js';
+import { collectFiles } from '../../src/domain/graph/builder/stages/collect-files.js';
 
 let tmpDir;
 
diff --git a/tests/builder/context.test.js b/tests/builder/context.test.js
index d691ab5a..360d287d 100644
--- a/tests/builder/context.test.js
+++ b/tests/builder/context.test.js
@@ -2,7 +2,7 @@
  * Unit tests for PipelineContext.
  */
 import { describe, expect, it } from 'vitest';
-import { PipelineContext } from '../../src/builder/context.js';
+import { PipelineContext } from '../../src/domain/graph/builder/context.js';
 
 describe('PipelineContext', () => {
   it('creates an instance with default values', () => {
diff --git a/tests/builder/detect-changes.test.js b/tests/builder/detect-changes.test.js
index ec0734d3..f6a671e3 100644
--- a/tests/builder/detect-changes.test.js
+++ b/tests/builder/detect-changes.test.js
@@ -5,9 +5,9 @@ import fs from 'node:fs';
 import os from 'node:os';
 import path from 'node:path';
 import { afterAll, beforeAll, describe, expect, it } from 'vitest';
-import { PipelineContext } from '../../src/builder/context.js';
-import { detectChanges } from '../../src/builder/stages/detect-changes.js';
-import { closeDb, initSchema, openDb } from '../../src/db.js';
+import { closeDb, initSchema, openDb } from '../../src/db/index.js';
+import { PipelineContext } from '../../src/domain/graph/builder/context.js';
+import { detectChanges } from '../../src/domain/graph/builder/stages/detect-changes.js';
 import { writeJournalHeader } from '../../src/journal.js';
 
 let tmpDir;
diff --git a/tests/builder/pipeline.test.js b/tests/builder/pipeline.test.js
index d6b8b76b..2fe0c283 100644
--- a/tests/builder/pipeline.test.js
+++ b/tests/builder/pipeline.test.js
@@ -8,7 +8,7 @@ import fs from 'node:fs';
 import os from 'node:os';
 import path from 'node:path';
 import { afterAll, beforeAll, describe, expect, it } from 'vitest';
-import { buildGraph } from '../../src/builder/pipeline.js';
+import { buildGraph } from '../../src/domain/graph/builder/pipeline.js';
 
 const FIXTURE_DIR = path.join(import.meta.dirname, '..', 'fixtures', 'sample-project');
 let tmpDir;
@@ -73,7 +73,7 @@ describe('buildGraph pipeline', () => {
 
   it('exports from barrel are identical to direct import', async () => {
     // Verify the barrel re-export works
-    const { buildGraph: fromBarrel } = await import('../../src/builder.js');
+    const { buildGraph: fromBarrel } = await import('../../src/domain/graph/builder.js');
     expect(fromBarrel).toBe(buildGraph);
   });
 });
diff --git a/tests/engines/dataflow-parity.test.js b/tests/engines/dataflow-parity.test.js
index ae08b92a..1559243a 100644
--- a/tests/engines/dataflow-parity.test.js
+++ b/tests/engines/dataflow-parity.test.js
@@ -12,7 +12,7 @@
  */
 
 import { beforeAll, describe, expect, it } from 'vitest';
-import { extractDataflow } from '../../src/dataflow.js';
+import { extractDataflow } from '../../src/features/dataflow.js';
 import { isNativeAvailable } from '../../src/native.js';
 import { createParsers, getParser } from '../../src/parser.js';
 
diff --git a/tests/graph/builders/dependency.test.js b/tests/graph/builders/dependency.test.js
index 18d46a77..6afb68de 100644
--- a/tests/graph/builders/dependency.test.js
+++ b/tests/graph/builders/dependency.test.js
@@ -1,6 +1,6 @@
 import Database from 'better-sqlite3';
 import { describe, expect, it } from 'vitest';
-import { initSchema } from '../../../src/db.js';
+import { initSchema } from '../../../src/db/index.js';
 import { buildDependencyGraph } from '../../../src/graph/builders/dependency.js';
 
 function createTestDb() {
diff --git a/tests/graph/builders/structure.test.js b/tests/graph/builders/structure.test.js
index 6d700b8a..dee6395f 100644
--- a/tests/graph/builders/structure.test.js
+++ b/tests/graph/builders/structure.test.js
@@ -1,6 +1,6 @@
 import Database from 'better-sqlite3';
 import { describe, expect, it } from 'vitest';
-import { initSchema } from '../../../src/db.js';
+import { initSchema } from '../../../src/db/index.js';
 import { buildStructureGraph } from '../../../src/graph/builders/structure.js';
 
 function createTestDb() {
diff --git a/tests/graph/builders/temporal.test.js b/tests/graph/builders/temporal.test.js
index be650681..cd602b0a 100644
--- a/tests/graph/builders/temporal.test.js
+++ b/tests/graph/builders/temporal.test.js
@@ -1,6 +1,6 @@
 import Database from 'better-sqlite3';
 import { describe, expect, it } from 'vitest';
-import { initSchema } from '../../../src/db.js';
+import { initSchema } from '../../../src/db/index.js';
 import { buildTemporalGraph } from '../../../src/graph/builders/temporal.js';
 
 function createTestDb() {
diff --git a/tests/graph/cycles.test.js b/tests/graph/cycles.test.js
index 915baf39..8f6946e3 100644
--- a/tests/graph/cycles.test.js
+++ b/tests/graph/cycles.test.js
@@ -4,8 +4,8 @@
 
 import Database from 'better-sqlite3';
 import { describe, expect, it } from 'vitest';
-import { findCycles, findCyclesJS } from '../../src/cycles.js';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
+import { findCycles, findCyclesJS } from '../../src/domain/graph/cycles.js';
 import { isNativeAvailable, loadNative } from '../../src/native.js';
 
 const hasNative = isNativeAvailable();
@@ -123,13 +123,13 @@ describe('findCycles — function-level', () => {
 
 describe('formatCycles', () => {
   it('returns no-cycles message for empty array', () => {
-    const { formatCycles } = require('../../src/cycles.js');
+    const { formatCycles } = require('../../src/domain/graph/cycles.js');
     const output = formatCycles([]);
     expect(output.toLowerCase()).toMatch(/no.*circular/);
   });
 
   it('formats a single cycle with all member files', () => {
-    const { formatCycles } = require('../../src/cycles.js');
+    const { formatCycles } = require('../../src/domain/graph/cycles.js');
     const output = formatCycles([['a.js', 'b.js']]);
     expect(output).toContain('a.js');
     expect(output).toContain('b.js');
@@ -137,7 +137,7 @@ describe('formatCycles', () => {
   });
 
   it('formats multiple cycles with distinct labels', () => {
-    const { formatCycles } = require('../../src/cycles.js');
+    const { formatCycles } = require('../../src/domain/graph/cycles.js');
     const output = formatCycles([
       ['a.js', 'b.js'],
       ['x.js', 'y.js', 'z.js'],
diff --git a/tests/graph/export.test.js b/tests/graph/export.test.js
index 3a12970e..fa3d4e11 100644
--- a/tests/graph/export.test.js
+++ b/tests/graph/export.test.js
@@ -4,7 +4,7 @@
 
 import Database from 'better-sqlite3';
 import { describe, expect, it } from 'vitest';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
 import {
   exportDOT,
   exportGraphML,
@@ -12,7 +12,7 @@ import {
   exportJSON,
   exportMermaid,
   exportNeo4jCSV,
-} from '../../src/export.js';
+} from '../../src/features/export.js';
 
 function createTestDb() {
   const db = new Database(':memory:');
diff --git a/tests/graph/viewer.test.js b/tests/graph/viewer.test.js
index 0ace2b01..95a67190 100644
--- a/tests/graph/viewer.test.js
+++ b/tests/graph/viewer.test.js
@@ -4,8 +4,8 @@
 
 import Database from 'better-sqlite3';
 import { describe, expect, it } from 'vitest';
-import { initSchema } from '../../src/db.js';
-import { generatePlotHTML, loadPlotConfig, prepareGraphData } from '../../src/viewer.js';
+import { initSchema } from '../../src/db/index.js';
+import { generatePlotHTML, loadPlotConfig, prepareGraphData } from '../../src/features/viewer.js';
 
 function createTestDb() {
   const db = new Database(':memory:');
diff --git a/tests/integration/ast.test.js b/tests/integration/ast.test.js
index 60cee696..706684d9 100644
--- a/tests/integration/ast.test.js
+++ b/tests/integration/ast.test.js
@@ -9,8 +9,8 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { AST_NODE_KINDS, astQueryData } from '../../src/ast.js';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
+import { AST_NODE_KINDS, astQueryData } from '../../src/features/ast.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/integration/audit.test.js b/tests/integration/audit.test.js
index 1664f7df..f6d00768 100644
--- a/tests/integration/audit.test.js
+++ b/tests/integration/audit.test.js
@@ -4,8 +4,8 @@ import path from 'node:path';
 import Database from 'better-sqlite3';
 
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { auditData } from '../../src/audit.js';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
+import { auditData } from '../../src/features/audit.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/integration/batch.test.js b/tests/integration/batch.test.js
index a4c5e6db..e903645c 100644
--- a/tests/integration/batch.test.js
+++ b/tests/integration/batch.test.js
@@ -17,8 +17,13 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { BATCH_COMMANDS, batchData, multiBatchData, splitTargets } from '../../src/batch.js';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
+import {
+  BATCH_COMMANDS,
+  batchData,
+  multiBatchData,
+  splitTargets,
+} from '../../src/features/batch.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/integration/branch-compare.test.js b/tests/integration/branch-compare.test.js
index 46c56c3c..0a276117 100644
--- a/tests/integration/branch-compare.test.js
+++ b/tests/integration/branch-compare.test.js
@@ -10,7 +10,7 @@ import fs from 'node:fs';
 import os from 'node:os';
 import path from 'node:path';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { branchCompareData, branchCompareMermaid } from '../../src/branch-compare.js';
+import { branchCompareData, branchCompareMermaid } from '../../src/features/branch-compare.js';
 
 let tmpDir;
 
diff --git a/tests/integration/build-parity.test.js b/tests/integration/build-parity.test.js
index d2f2e8a8..18c710e2 100644
--- a/tests/integration/build-parity.test.js
+++ b/tests/integration/build-parity.test.js
@@ -12,7 +12,7 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, it } from 'vitest';
-import { buildGraph } from '../../src/builder.js';
+import { buildGraph } from '../../src/domain/graph/builder.js';
 import { isNativeAvailable } from '../../src/native.js';
 
 const FIXTURE_DIR = path.join(import.meta.dirname, '..', 'fixtures', 'sample-project');
diff --git a/tests/integration/build.test.js b/tests/integration/build.test.js
index 3669cdb3..8af7600d 100644
--- a/tests/integration/build.test.js
+++ b/tests/integration/build.test.js
@@ -8,8 +8,8 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { buildGraph } from '../../src/builder.js';
-import { closeDb, openDb, setBuildMeta } from '../../src/db.js';
+import { closeDb, openDb, setBuildMeta } from '../../src/db/index.js';
+import { buildGraph } from '../../src/domain/graph/builder.js';
 import { JOURNAL_FILENAME, writeJournalHeader } from '../../src/journal.js';
 
 // ES-module versions of the sample-project fixture so the parser
diff --git a/tests/integration/cfg.test.js b/tests/integration/cfg.test.js
index 3fdbeab0..548042ea 100644
--- a/tests/integration/cfg.test.js
+++ b/tests/integration/cfg.test.js
@@ -9,8 +9,8 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { cfgData, cfgToDOT, cfgToMermaid } from '../../src/cfg.js';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
+import { cfgData, cfgToDOT, cfgToMermaid } from '../../src/features/cfg.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/integration/check.test.js b/tests/integration/check.test.js
index feb5921b..1e339188 100644
--- a/tests/integration/check.test.js
+++ b/tests/integration/check.test.js
@@ -10,6 +10,7 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
+import { initSchema } from '../../src/db/index.js';
 import {
   checkData,
   checkMaxBlastRadius,
@@ -17,8 +18,7 @@ import {
   checkNoNewCycles,
   checkNoSignatureChanges,
   parseDiffOutput,
-} from '../../src/check.js';
-import { initSchema } from '../../src/db.js';
+} from '../../src/features/check.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/integration/cochange.test.js b/tests/integration/cochange.test.js
index e1a9ad51..4b60e893 100644
--- a/tests/integration/cochange.test.js
+++ b/tests/integration/cochange.test.js
@@ -12,13 +12,13 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
+import { initSchema } from '../../src/db/index.js';
 import {
   coChangeData,
   coChangeTopData,
   computeCoChanges,
   scanGitHistory,
-} from '../../src/cochange.js';
-import { initSchema } from '../../src/db.js';
+} from '../../src/features/cochange.js';
 
 // ─── A. computeCoChanges (pure logic) ────────────────────────────────
 
diff --git a/tests/integration/communities.test.js b/tests/integration/communities.test.js
index cdd1224e..3981beb2 100644
--- a/tests/integration/communities.test.js
+++ b/tests/integration/communities.test.js
@@ -14,8 +14,8 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { communitiesData, communitySummaryForStats } from '../../src/communities.js';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
+import { communitiesData, communitySummaryForStats } from '../../src/features/communities.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/integration/complexity.test.js b/tests/integration/complexity.test.js
index 5ec66107..52454bd9 100644
--- a/tests/integration/complexity.test.js
+++ b/tests/integration/complexity.test.js
@@ -10,9 +10,9 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test, vi } from 'vitest';
-import { complexityData } from '../../src/complexity.js';
 import { loadConfig } from '../../src/config.js';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
+import { complexityData } from '../../src/features/complexity.js';
 
 vi.mock('../../src/config.js', () => ({
   loadConfig: vi.fn(() => ({})),
diff --git a/tests/integration/context.test.js b/tests/integration/context.test.js
index fd2779a7..e9b1afc0 100644
--- a/tests/integration/context.test.js
+++ b/tests/integration/context.test.js
@@ -10,8 +10,8 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { initSchema } from '../../src/db.js';
-import { contextData } from '../../src/queries.js';
+import { initSchema } from '../../src/db/index.js';
+import { contextData } from '../../src/domain/queries.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/integration/dataflow.test.js b/tests/integration/dataflow.test.js
index 910dca76..1659fdce 100644
--- a/tests/integration/dataflow.test.js
+++ b/tests/integration/dataflow.test.js
@@ -16,8 +16,8 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { dataflowData, dataflowImpactData, dataflowPathData } from '../../src/dataflow.js';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
+import { dataflowData, dataflowImpactData, dataflowPathData } from '../../src/features/dataflow.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/integration/exports.test.js b/tests/integration/exports.test.js
index b7793c86..623f19b6 100644
--- a/tests/integration/exports.test.js
+++ b/tests/integration/exports.test.js
@@ -28,8 +28,8 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { initSchema } from '../../src/db.js';
-import { exportsData } from '../../src/queries.js';
+import { initSchema } from '../../src/db/index.js';
+import { exportsData } from '../../src/domain/queries.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/integration/flow.test.js b/tests/integration/flow.test.js
index 0ff8e5f2..97d83515 100644
--- a/tests/integration/flow.test.js
+++ b/tests/integration/flow.test.js
@@ -17,9 +17,9 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { initSchema } from '../../src/db.js';
-import { entryPointType, flowData, listEntryPointsData } from '../../src/flow.js';
-import { classifyNodeRoles, FRAMEWORK_ENTRY_PREFIXES } from '../../src/structure.js';
+import { initSchema } from '../../src/db/index.js';
+import { entryPointType, flowData, listEntryPointsData } from '../../src/features/flow.js';
+import { classifyNodeRoles, FRAMEWORK_ENTRY_PREFIXES } from '../../src/features/structure.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/integration/incremental-parity.test.js b/tests/integration/incremental-parity.test.js
index a109471f..555975b8 100644
--- a/tests/integration/incremental-parity.test.js
+++ b/tests/integration/incremental-parity.test.js
@@ -11,7 +11,7 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, it } from 'vitest';
-import { buildGraph } from '../../src/builder.js';
+import { buildGraph } from '../../src/domain/graph/builder.js';
 
 const FIXTURE_DIR = path.join(import.meta.dirname, '..', 'fixtures', 'barrel-project');
 
diff --git a/tests/integration/manifesto.test.js b/tests/integration/manifesto.test.js
index 755f240d..d9b5d93f 100644
--- a/tests/integration/manifesto.test.js
+++ b/tests/integration/manifesto.test.js
@@ -10,8 +10,8 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { initSchema } from '../../src/db.js';
-import { manifestoData, RULE_DEFS } from '../../src/manifesto.js';
+import { initSchema } from '../../src/db/index.js';
+import { manifestoData, RULE_DEFS } from '../../src/features/manifesto.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/integration/owners.test.js b/tests/integration/owners.test.js
index 35ad147c..7d26f958 100644
--- a/tests/integration/owners.test.js
+++ b/tests/integration/owners.test.js
@@ -3,8 +3,8 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { initSchema } from '../../src/db.js';
-import { ownersData, ownersForFiles } from '../../src/owners.js';
+import { initSchema } from '../../src/db/index.js';
+import { ownersData, ownersForFiles } from '../../src/features/owners.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/integration/pagination.test.js b/tests/integration/pagination.test.js
index f938ee1c..e57f9c19 100644
--- a/tests/integration/pagination.test.js
+++ b/tests/integration/pagination.test.js
@@ -18,16 +18,7 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { initSchema } from '../../src/db.js';
-import { exportDOT, exportJSON, exportMermaid } from '../../src/export.js';
-import { listEntryPointsData } from '../../src/flow.js';
-import {
-  MCP_DEFAULTS,
-  MCP_MAX_LIMIT,
-  paginate,
-  paginateResult,
-  printNdjson,
-} from '../../src/paginate.js';
+import { initSchema } from '../../src/db/index.js';
 import {
   contextData,
   explainData,
@@ -41,7 +32,16 @@ import {
   queryNameData,
   rolesData,
   whereData,
-} from '../../src/queries.js';
+} from '../../src/domain/queries.js';
+import { exportDOT, exportJSON, exportMermaid } from '../../src/features/export.js';
+import { listEntryPointsData } from '../../src/features/flow.js';
+import {
+  MCP_DEFAULTS,
+  MCP_MAX_LIMIT,
+  paginate,
+  paginateResult,
+  printNdjson,
+} from '../../src/paginate.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/integration/qualified-names.test.js b/tests/integration/qualified-names.test.js
index 0ea987a2..3fc1beae 100644
--- a/tests/integration/qualified-names.test.js
+++ b/tests/integration/qualified-names.test.js
@@ -2,10 +2,14 @@ import fs from 'node:fs';
 import os from 'node:os';
 import path from 'node:path';
 import { afterAll, beforeAll, describe, expect, it } from 'vitest';
-import { buildGraph } from '../../src/builder.js';
-import { findNodeByQualifiedName, findNodesByScope, openReadonlyOrFail } from '../../src/db.js';
+import {
+  findNodeByQualifiedName,
+  findNodesByScope,
+  openReadonlyOrFail,
+} from '../../src/db/index.js';
+import { buildGraph } from '../../src/domain/graph/builder.js';
+import { childrenData } from '../../src/domain/queries.js';
 import { pythonVisibility } from '../../src/extractors/helpers.js';
-import { childrenData } from '../../src/queries.js';
 
 // Fixture: a small project with classes, methods, and visibility modifiers
 const FIXTURE_FILES = {
diff --git a/tests/integration/queries.test.js b/tests/integration/queries.test.js
index 788bb117..282ee84e 100644
--- a/tests/integration/queries.test.js
+++ b/tests/integration/queries.test.js
@@ -24,7 +24,7 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
 import {
   diffImpactData,
   explainData,
@@ -39,7 +39,7 @@ import {
   queryNameData,
   statsData,
   whereData,
-} from '../../src/queries.js';
+} from '../../src/domain/queries.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/integration/roles.test.js b/tests/integration/roles.test.js
index c76b5719..2a92b16a 100644
--- a/tests/integration/roles.test.js
+++ b/tests/integration/roles.test.js
@@ -12,15 +12,15 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
 import {
   explainData,
   listFunctionsData,
   rolesData,
   statsData,
   whereData,
-} from '../../src/queries.js';
-import { classifyNodeRoles } from '../../src/structure.js';
+} from '../../src/domain/queries.js';
+import { classifyNodeRoles } from '../../src/features/structure.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/integration/scoped-rebuild.test.js b/tests/integration/scoped-rebuild.test.js
index fd4d8a12..9b6d699b 100644
--- a/tests/integration/scoped-rebuild.test.js
+++ b/tests/integration/scoped-rebuild.test.js
@@ -10,7 +10,7 @@ import fs from 'node:fs';
 import os from 'node:os';
 import path from 'node:path';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { buildGraph } from '../../src/builder.js';
+import { buildGraph } from '../../src/domain/graph/builder.js';
 
 const FIXTURE_DIR = path.join(import.meta.dirname, '..', 'fixtures', 'sample-project');
 
diff --git a/tests/integration/sequence.test.js b/tests/integration/sequence.test.js
index 6d3367e4..fade9cca 100644
--- a/tests/integration/sequence.test.js
+++ b/tests/integration/sequence.test.js
@@ -19,8 +19,8 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { initSchema } from '../../src/db.js';
-import { sequenceData, sequenceToMermaid } from '../../src/sequence.js';
+import { initSchema } from '../../src/db/index.js';
+import { sequenceData, sequenceToMermaid } from '../../src/features/sequence.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/integration/structure.test.js b/tests/integration/structure.test.js
index 5dae68f6..fe97a118 100644
--- a/tests/integration/structure.test.js
+++ b/tests/integration/structure.test.js
@@ -8,8 +8,8 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { buildGraph } from '../../src/builder.js';
-import { hotspotsData, moduleBoundariesData, structureData } from '../../src/structure.js';
+import { buildGraph } from '../../src/domain/graph/builder.js';
+import { hotspotsData, moduleBoundariesData, structureData } from '../../src/features/structure.js';
 
 // Multi-directory fixture with cross-directory imports
 const FIXTURE_FILES = {
diff --git a/tests/integration/triage.test.js b/tests/integration/triage.test.js
index f9727d5b..47192cf3 100644
--- a/tests/integration/triage.test.js
+++ b/tests/integration/triage.test.js
@@ -10,7 +10,7 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { triageData } from '../../src/triage.js';
+import { triageData } from '../../src/features/triage.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
@@ -57,7 +57,7 @@ let tmpDir, dbPath;
 let fnHigh, fnMed, fnLow, fnTest, fnClass;
 
 beforeAll(async () => {
-  const { initSchema } = await import('../../src/db.js');
+  const { initSchema } = await import('../../src/db/index.js');
 
   tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-triage-'));
   fs.mkdirSync(path.join(tmpDir, '.codegraph'));
@@ -286,7 +286,7 @@ describe('triage', () => {
     fs.mkdirSync(path.join(sparseDir, '.codegraph'));
     const sparseDbPath = path.join(sparseDir, '.codegraph', 'graph.db');
 
-    const { initSchema } = await import('../../src/db.js');
+    const { initSchema } = await import('../../src/db/index.js');
     const db = new Database(sparseDbPath);
     db.pragma('journal_mode = WAL');
     initSchema(db);
diff --git a/tests/parsers/ast-all-langs.test.js b/tests/parsers/ast-all-langs.test.js
index 8021aeb0..615c9304 100644
--- a/tests/parsers/ast-all-langs.test.js
+++ b/tests/parsers/ast-all-langs.test.js
@@ -12,8 +12,8 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { buildAstNodes } from '../../src/ast.js';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
+import { buildAstNodes } from '../../src/features/ast.js';
 import { loadNative } from '../../src/native.js';
 import { parseFilesAuto } from '../../src/parser.js';
 
diff --git a/tests/parsers/ast-nodes.test.js b/tests/parsers/ast-nodes.test.js
index 93b1e1be..894d9d1a 100644
--- a/tests/parsers/ast-nodes.test.js
+++ b/tests/parsers/ast-nodes.test.js
@@ -10,8 +10,8 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { buildAstNodes } from '../../src/ast.js';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
+import { buildAstNodes } from '../../src/features/ast.js';
 import { loadNative } from '../../src/native.js';
 import { parseFilesAuto } from '../../src/parser.js';
 
diff --git a/tests/parsers/cfg-all-langs.test.js b/tests/parsers/cfg-all-langs.test.js
index d8dd1de7..f19ab8ec 100644
--- a/tests/parsers/cfg-all-langs.test.js
+++ b/tests/parsers/cfg-all-langs.test.js
@@ -13,9 +13,9 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
-import { buildCFGData, buildFunctionCFG } from '../../src/cfg.js';
-import { COMPLEXITY_RULES, findFunctionNode } from '../../src/complexity.js';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
+import { buildCFGData, buildFunctionCFG } from '../../src/features/cfg.js';
+import { COMPLEXITY_RULES, findFunctionNode } from '../../src/features/complexity.js';
 import { loadNative } from '../../src/native.js';
 import { createParsers, getParser, parseFilesAuto } from '../../src/parser.js';
 
diff --git a/tests/parsers/dataflow-csharp.test.js b/tests/parsers/dataflow-csharp.test.js
index 2e3249ad..6744d1c9 100644
--- a/tests/parsers/dataflow-csharp.test.js
+++ b/tests/parsers/dataflow-csharp.test.js
@@ -2,7 +2,7 @@
  * Unit tests for extractDataflow() against parsed C# ASTs.
  */
 import { beforeAll, describe, expect, it } from 'vitest';
-import { extractDataflow } from '../../src/dataflow.js';
+import { extractDataflow } from '../../src/features/dataflow.js';
 import { createParsers } from '../../src/parser.js';
 
 describe('extractDataflow — C#', () => {
diff --git a/tests/parsers/dataflow-go.test.js b/tests/parsers/dataflow-go.test.js
index 040f671a..674b8b3c 100644
--- a/tests/parsers/dataflow-go.test.js
+++ b/tests/parsers/dataflow-go.test.js
@@ -2,7 +2,7 @@
  * Unit tests for extractDataflow() against parsed Go ASTs.
  */
 import { beforeAll, describe, expect, it } from 'vitest';
-import { extractDataflow } from '../../src/dataflow.js';
+import { extractDataflow } from '../../src/features/dataflow.js';
 import { createParsers } from '../../src/parser.js';
 
 describe('extractDataflow — Go', () => {
diff --git a/tests/parsers/dataflow-java.test.js b/tests/parsers/dataflow-java.test.js
index b62c999f..24175ea0 100644
--- a/tests/parsers/dataflow-java.test.js
+++ b/tests/parsers/dataflow-java.test.js
@@ -2,7 +2,7 @@
  * Unit tests for extractDataflow() against parsed Java ASTs.
  */
 import { beforeAll, describe, expect, it } from 'vitest';
-import { extractDataflow } from '../../src/dataflow.js';
+import { extractDataflow } from '../../src/features/dataflow.js';
 import { createParsers } from '../../src/parser.js';
 
 describe('extractDataflow — Java', () => {
diff --git a/tests/parsers/dataflow-javascript.test.js b/tests/parsers/dataflow-javascript.test.js
index e4c2d58d..df9d1dfb 100644
--- a/tests/parsers/dataflow-javascript.test.js
+++ b/tests/parsers/dataflow-javascript.test.js
@@ -2,7 +2,7 @@
  * Unit tests for extractDataflow() against parsed JS/TS ASTs.
  */
 import { beforeAll, describe, expect, it } from 'vitest';
-import { extractDataflow } from '../../src/dataflow.js';
+import { extractDataflow } from '../../src/features/dataflow.js';
 import { createParsers } from '../../src/parser.js';
 
 describe('extractDataflow — JavaScript', () => {
diff --git a/tests/parsers/dataflow-php.test.js b/tests/parsers/dataflow-php.test.js
index 8d1d4cb3..ae337942 100644
--- a/tests/parsers/dataflow-php.test.js
+++ b/tests/parsers/dataflow-php.test.js
@@ -2,7 +2,7 @@
  * Unit tests for extractDataflow() against parsed PHP ASTs.
  */
 import { beforeAll, describe, expect, it } from 'vitest';
-import { extractDataflow } from '../../src/dataflow.js';
+import { extractDataflow } from '../../src/features/dataflow.js';
 import { createParsers } from '../../src/parser.js';
 
 describe('extractDataflow — PHP', () => {
diff --git a/tests/parsers/dataflow-python.test.js b/tests/parsers/dataflow-python.test.js
index 0fdf1c74..4a83874e 100644
--- a/tests/parsers/dataflow-python.test.js
+++ b/tests/parsers/dataflow-python.test.js
@@ -2,7 +2,7 @@
  * Unit tests for extractDataflow() against parsed Python ASTs.
  */
 import { beforeAll, describe, expect, it } from 'vitest';
-import { extractDataflow } from '../../src/dataflow.js';
+import { extractDataflow } from '../../src/features/dataflow.js';
 import { createParsers } from '../../src/parser.js';
 
 describe('extractDataflow — Python', () => {
diff --git a/tests/parsers/dataflow-ruby.test.js b/tests/parsers/dataflow-ruby.test.js
index 110bf2ab..69aa67db 100644
--- a/tests/parsers/dataflow-ruby.test.js
+++ b/tests/parsers/dataflow-ruby.test.js
@@ -2,7 +2,7 @@
  * Unit tests for extractDataflow() against parsed Ruby ASTs.
  */
 import { beforeAll, describe, expect, it } from 'vitest';
-import { extractDataflow } from '../../src/dataflow.js';
+import { extractDataflow } from '../../src/features/dataflow.js';
 import { createParsers } from '../../src/parser.js';
 
 describe('extractDataflow — Ruby', () => {
diff --git a/tests/parsers/dataflow-rust.test.js b/tests/parsers/dataflow-rust.test.js
index c1437146..5d771740 100644
--- a/tests/parsers/dataflow-rust.test.js
+++ b/tests/parsers/dataflow-rust.test.js
@@ -2,7 +2,7 @@
  * Unit tests for extractDataflow() against parsed Rust ASTs.
  */
 import { beforeAll, describe, expect, it } from 'vitest';
-import { extractDataflow } from '../../src/dataflow.js';
+import { extractDataflow } from '../../src/features/dataflow.js';
 import { createParsers } from '../../src/parser.js';
 
 describe('extractDataflow — Rust', () => {
diff --git a/tests/resolution/parity.test.js b/tests/resolution/parity.test.js
index 08adc839..444c4040 100644
--- a/tests/resolution/parity.test.js
+++ b/tests/resolution/parity.test.js
@@ -6,7 +6,6 @@ import fs from 'node:fs';
 import os from 'node:os';
 import path from 'node:path';
 import { describe, expect, it } from 'vitest';
-import { isNativeAvailable, loadNative } from '../../src/native.js';
 import {
   computeConfidence,
   computeConfidenceJS,
@@ -14,7 +13,8 @@ import {
   resolveImportPath,
   resolveImportPathJS,
   resolveImportsBatch,
-} from '../../src/resolve.js';
+} from '../../src/domain/graph/resolve.js';
+import { isNativeAvailable, loadNative } from '../../src/native.js';
 
 const hasNative = isNativeAvailable();
 
diff --git a/tests/search/embedder-search.test.js b/tests/search/embedder-search.test.js
index 86fe5543..f873a33b 100644
--- a/tests/search/embedder-search.test.js
+++ b/tests/search/embedder-search.test.js
@@ -3,7 +3,7 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test, vi } from 'vitest';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
 
 // ─── Mock setup ────────────────────────────────────────────────────────
 
@@ -38,7 +38,7 @@ import {
   multiSearchData,
   search,
   searchData,
-} from '../../src/embeddings/index.js';
+} from '../../src/domain/search/index.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/search/embedding-regression.test.js b/tests/search/embedding-regression.test.js
index 56222875..8e618185 100644
--- a/tests/search/embedding-regression.test.js
+++ b/tests/search/embedding-regression.test.js
@@ -22,8 +22,8 @@ try {
 }
 
 // Lazy-import to avoid top-level errors when transformers is missing
-const { buildGraph } = await import('../../src/builder.js');
-const { buildEmbeddings, searchData } = await import('../../src/embeddings/index.js');
+const { buildGraph } = await import('../../src/domain/graph/builder.js');
+const { buildEmbeddings, searchData } = await import('../../src/domain/search/index.js');
 
 // Same ES-module fixture files used by build.test.js
 const FIXTURE_FILES = {
diff --git a/tests/search/embedding-strategy.test.js b/tests/search/embedding-strategy.test.js
index 70215559..a8a50a2c 100644
--- a/tests/search/embedding-strategy.test.js
+++ b/tests/search/embedding-strategy.test.js
@@ -3,7 +3,7 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test, vi } from 'vitest';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
 
 // ─── Mock setup ────────────────────────────────────────────────────────
 
@@ -31,7 +31,7 @@ import {
   EMBEDDING_STRATEGIES,
   estimateTokens,
   MODELS,
-} from '../../src/embeddings/index.js';
+} from '../../src/domain/search/index.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/unit/boundaries.test.js b/tests/unit/boundaries.test.js
index 6dfe1e12..0f2642e7 100644
--- a/tests/unit/boundaries.test.js
+++ b/tests/unit/boundaries.test.js
@@ -3,14 +3,14 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, test } from 'vitest';
+import { initSchema } from '../../src/db/index.js';
 import {
   evaluateBoundaries,
   globToRegex,
   PRESETS,
   resolveModules,
   validateBoundaryConfig,
-} from '../../src/boundaries.js';
-import { initSchema } from '../../src/db.js';
+} from '../../src/features/boundaries.js';
 
 // ─── globToRegex ─────────────────────────────────────────────────────
 
diff --git a/tests/unit/builder.test.js b/tests/unit/builder.test.js
index 63c60a4c..7dc7d958 100644
--- a/tests/unit/builder.test.js
+++ b/tests/unit/builder.test.js
@@ -9,7 +9,7 @@ import fs from 'node:fs';
 import os from 'node:os';
 import path from 'node:path';
 import { afterAll, beforeAll, describe, expect, it, vi } from 'vitest';
-import { collectFiles, loadPathAliases, readFileSafe } from '../../src/builder.js';
+import { collectFiles, loadPathAliases, readFileSafe } from '../../src/domain/graph/builder.js';
 
 let tmpDir;
 
diff --git a/tests/unit/cfg.test.js b/tests/unit/cfg.test.js
index 7a19a457..adf8aa49 100644
--- a/tests/unit/cfg.test.js
+++ b/tests/unit/cfg.test.js
@@ -9,8 +9,8 @@ import { beforeAll, describe, expect, it } from 'vitest';
 import { CFG_RULES } from '../../src/ast-analysis/rules/index.js';
 import { walkWithVisitors } from '../../src/ast-analysis/visitor.js';
 import { createCfgVisitor } from '../../src/ast-analysis/visitors/cfg-visitor.js';
-import { buildFunctionCFG, makeCfgRules } from '../../src/cfg.js';
-import { COMPLEXITY_RULES } from '../../src/complexity.js';
+import { buildFunctionCFG, makeCfgRules } from '../../src/features/cfg.js';
+import { COMPLEXITY_RULES } from '../../src/features/complexity.js';
 import { createParsers } from '../../src/parser.js';
 
 let jsParser;
diff --git a/tests/unit/complexity.test.js b/tests/unit/complexity.test.js
index d3b4b73f..b458ead1 100644
--- a/tests/unit/complexity.test.js
+++ b/tests/unit/complexity.test.js
@@ -13,7 +13,7 @@ import {
   computeLOCMetrics,
   computeMaintainabilityIndex,
   HALSTEAD_RULES,
-} from '../../src/complexity.js';
+} from '../../src/features/complexity.js';
 import { createParsers } from '../../src/parser.js';
 
 let jsParser;
diff --git a/tests/unit/db.test.js b/tests/unit/db.test.js
index 47dc393d..7d338971 100644
--- a/tests/unit/db.test.js
+++ b/tests/unit/db.test.js
@@ -16,7 +16,7 @@ import {
   openDb,
   openReadonlyOrFail,
   setBuildMeta,
-} from '../../src/db.js';
+} from '../../src/db/index.js';
 
 let tmpDir;
 
diff --git a/tests/unit/mcp.test.js b/tests/unit/mcp.test.js
index 94149c0a..cb9f490e 100644
--- a/tests/unit/mcp.test.js
+++ b/tests/unit/mcp.test.js
@@ -6,7 +6,7 @@
  */
 
 import { beforeEach, describe, expect, it, vi } from 'vitest';
-import { buildToolList, TOOLS } from '../../src/mcp.js';
+import { buildToolList, TOOLS } from '../../src/mcp/index.js';
 
 const ALL_TOOL_NAMES = [
   'query',
@@ -281,7 +281,7 @@ describe('startMCPServer handler dispatch', () => {
     }));
 
     // Mock query functions
-    vi.doMock('../../src/queries.js', () => ({
+    vi.doMock('../../src/domain/queries.js', () => ({
       EVERY_SYMBOL_KIND: [],
       EVERY_EDGE_KIND: [],
       VALID_ROLES: [],
@@ -309,7 +309,7 @@ describe('startMCPServer handler dispatch', () => {
     }));
 
     // Clear module cache and reimport
-    const { startMCPServer } = await import('../../src/mcp.js');
+    const { startMCPServer } = await import('../../src/mcp/index.js');
     await startMCPServer('/tmp/test.db');
 
     // Test tools/list — single-repo mode by default (no list_repos)
@@ -352,7 +352,7 @@ describe('startMCPServer handler dispatch', () => {
     }));
 
     const fnDepsMock = vi.fn(() => ({ name: 'myFn', results: [{ callers: [] }] }));
-    vi.doMock('../../src/queries.js', () => ({
+    vi.doMock('../../src/domain/queries.js', () => ({
       EVERY_SYMBOL_KIND: [],
       EVERY_EDGE_KIND: [],
       VALID_ROLES: [],
@@ -373,7 +373,7 @@ describe('startMCPServer handler dispatch', () => {
       pathData: vi.fn(() => ({ from: 'a', to: 'b', found: false })),
     }));
 
-    const { startMCPServer } = await import('../../src/mcp.js');
+    const { startMCPServer } = await import('../../src/mcp/index.js');
     await startMCPServer('/tmp/test.db');
 
     const result = await handlers['tools/call']({
@@ -413,7 +413,7 @@ describe('startMCPServer handler dispatch', () => {
     }));
 
     const fnImpactMock = vi.fn(() => ({ name: 'test', results: [] }));
-    vi.doMock('../../src/queries.js', () => ({
+    vi.doMock('../../src/domain/queries.js', () => ({
       EVERY_SYMBOL_KIND: [],
       EVERY_EDGE_KIND: [],
       VALID_ROLES: [],
@@ -434,7 +434,7 @@ describe('startMCPServer handler dispatch', () => {
       pathData: vi.fn(() => ({ from: 'a', to: 'b', found: false })),
     }));
 
-    const { startMCPServer } = await import('../../src/mcp.js');
+    const { startMCPServer } = await import('../../src/mcp/index.js');
     await startMCPServer('/tmp/test.db');
 
     const result = await handlers['tools/call']({
@@ -471,7 +471,7 @@ describe('startMCPServer handler dispatch', () => {
     }));
 
     const diffImpactMock = vi.fn(() => ({ changedFiles: 2, affectedFunctions: [] }));
-    vi.doMock('../../src/queries.js', () => ({
+    vi.doMock('../../src/domain/queries.js', () => ({
       EVERY_SYMBOL_KIND: [],
       EVERY_EDGE_KIND: [],
       VALID_ROLES: [],
@@ -492,7 +492,7 @@ describe('startMCPServer handler dispatch', () => {
       pathData: vi.fn(() => ({ from: 'a', to: 'b', found: false })),
     }));
 
-    const { startMCPServer } = await import('../../src/mcp.js');
+    const { startMCPServer } = await import('../../src/mcp/index.js');
     await startMCPServer('/tmp/test.db');
 
     const result = await handlers['tools/call']({
@@ -532,7 +532,7 @@ describe('startMCPServer handler dispatch', () => {
       count: 3,
       functions: [{ name: 'a' }, { name: 'b' }, { name: 'c' }],
     }));
-    vi.doMock('../../src/queries.js', () => ({
+    vi.doMock('../../src/domain/queries.js', () => ({
       EVERY_SYMBOL_KIND: [],
       EVERY_EDGE_KIND: [],
       VALID_ROLES: [],
@@ -553,7 +553,7 @@ describe('startMCPServer handler dispatch', () => {
       pathData: vi.fn(() => ({ from: 'a', to: 'b', found: false })),
     }));
 
-    const { startMCPServer } = await import('../../src/mcp.js');
+    const { startMCPServer } = await import('../../src/mcp/index.js');
     await startMCPServer('/tmp/test.db');
 
     const result = await handlers['tools/call']({
@@ -594,7 +594,7 @@ describe('startMCPServer handler dispatch', () => {
     }));
 
     const fnDepsMock = vi.fn(() => ({ name: 'test', results: [] }));
-    vi.doMock('../../src/queries.js', () => ({
+    vi.doMock('../../src/domain/queries.js', () => ({
       EVERY_SYMBOL_KIND: [],
       EVERY_EDGE_KIND: [],
       VALID_ROLES: [],
@@ -615,7 +615,7 @@ describe('startMCPServer handler dispatch', () => {
       pathData: vi.fn(() => ({ from: 'a', to: 'b', found: false })),
     }));
 
-    const { startMCPServer } = await import('../../src/mcp.js');
+    const { startMCPServer } = await import('../../src/mcp/index.js');
     await startMCPServer(undefined, { multiRepo: true });
 
     const result = await handlers['tools/call']({
@@ -653,7 +653,7 @@ describe('startMCPServer handler dispatch', () => {
     vi.doMock('../../src/registry.js', () => ({
       resolveRepoDbPath: vi.fn(() => undefined),
     }));
-    vi.doMock('../../src/queries.js', () => ({
+    vi.doMock('../../src/domain/queries.js', () => ({
       EVERY_SYMBOL_KIND: [],
       EVERY_EDGE_KIND: [],
       VALID_ROLES: [],
@@ -674,7 +674,7 @@ describe('startMCPServer handler dispatch', () => {
       pathData: vi.fn(() => ({ from: 'a', to: 'b', found: false })),
     }));
 
-    const { startMCPServer } = await import('../../src/mcp.js');
+    const { startMCPServer } = await import('../../src/mcp/index.js');
     await startMCPServer(undefined, { multiRepo: true });
 
     const result = await handlers['tools/call']({
@@ -706,7 +706,7 @@ describe('startMCPServer handler dispatch', () => {
     vi.doMock('../../src/registry.js', () => ({
       resolveRepoDbPath: vi.fn(() => '/some/path'),
     }));
-    vi.doMock('../../src/queries.js', () => ({
+    vi.doMock('../../src/domain/queries.js', () => ({
       EVERY_SYMBOL_KIND: [],
       EVERY_EDGE_KIND: [],
       VALID_ROLES: [],
@@ -727,7 +727,7 @@ describe('startMCPServer handler dispatch', () => {
       pathData: vi.fn(() => ({ from: 'a', to: 'b', found: false })),
     }));
 
-    const { startMCPServer } = await import('../../src/mcp.js');
+    const { startMCPServer } = await import('../../src/mcp/index.js');
     await startMCPServer(undefined, { allowedRepos: ['allowed-repo'] });
 
     const result = await handlers['tools/call']({
@@ -761,7 +761,7 @@ describe('startMCPServer handler dispatch', () => {
     }));
 
     const fnDepsMock = vi.fn(() => ({ name: 'test', results: [] }));
-    vi.doMock('../../src/queries.js', () => ({
+    vi.doMock('../../src/domain/queries.js', () => ({
       EVERY_SYMBOL_KIND: [],
       EVERY_EDGE_KIND: [],
       VALID_ROLES: [],
@@ -782,7 +782,7 @@ describe('startMCPServer handler dispatch', () => {
       pathData: vi.fn(() => ({ from: 'a', to: 'b', found: false })),
     }));
 
-    const { startMCPServer } = await import('../../src/mcp.js');
+    const { startMCPServer } = await import('../../src/mcp/index.js');
     await startMCPServer(undefined, { allowedRepos: ['my-repo'] });
 
     const result = await handlers['tools/call']({
@@ -826,7 +826,7 @@ describe('startMCPServer handler dispatch', () => {
       ]),
       pruneRegistry: vi.fn(),
     }));
-    vi.doMock('../../src/queries.js', () => ({
+    vi.doMock('../../src/domain/queries.js', () => ({
       EVERY_SYMBOL_KIND: [],
       EVERY_EDGE_KIND: [],
       VALID_ROLES: [],
@@ -847,7 +847,7 @@ describe('startMCPServer handler dispatch', () => {
       pathData: vi.fn(() => ({ from: 'a', to: 'b', found: false })),
     }));
 
-    const { startMCPServer } = await import('../../src/mcp.js');
+    const { startMCPServer } = await import('../../src/mcp/index.js');
     await startMCPServer(undefined, { allowedRepos: ['alpha', 'gamma'] });
 
     const result = await handlers['tools/call']({
@@ -884,7 +884,7 @@ describe('startMCPServer handler dispatch', () => {
       ]),
       pruneRegistry: vi.fn(),
     }));
-    vi.doMock('../../src/queries.js', () => ({
+    vi.doMock('../../src/domain/queries.js', () => ({
       EVERY_SYMBOL_KIND: [],
       EVERY_EDGE_KIND: [],
       VALID_ROLES: [],
@@ -905,7 +905,7 @@ describe('startMCPServer handler dispatch', () => {
       pathData: vi.fn(() => ({ from: 'a', to: 'b', found: false })),
     }));
 
-    const { startMCPServer } = await import('../../src/mcp.js');
+    const { startMCPServer } = await import('../../src/mcp/index.js');
     await startMCPServer(undefined, { multiRepo: true });
 
     const result = await handlers['tools/call']({
@@ -933,7 +933,7 @@ describe('startMCPServer handler dispatch', () => {
       ListToolsRequestSchema: 'tools/list',
       CallToolRequestSchema: 'tools/call',
     }));
-    vi.doMock('../../src/queries.js', () => ({
+    vi.doMock('../../src/domain/queries.js', () => ({
       EVERY_SYMBOL_KIND: [],
       EVERY_EDGE_KIND: [],
       VALID_ROLES: [],
@@ -954,7 +954,7 @@ describe('startMCPServer handler dispatch', () => {
       pathData: vi.fn(() => ({ from: 'a', to: 'b', found: false })),
     }));
 
-    const { startMCPServer } = await import('../../src/mcp.js');
+    const { startMCPServer } = await import('../../src/mcp/index.js');
     await startMCPServer('/tmp/test.db');
 
     const result = await handlers['tools/call']({
@@ -983,7 +983,7 @@ describe('startMCPServer handler dispatch', () => {
       ListToolsRequestSchema: 'tools/list',
       CallToolRequestSchema: 'tools/call',
     }));
-    vi.doMock('../../src/queries.js', () => ({
+    vi.doMock('../../src/domain/queries.js', () => ({
       EVERY_SYMBOL_KIND: [],
       EVERY_EDGE_KIND: [],
       VALID_ROLES: [],
@@ -1004,7 +1004,7 @@ describe('startMCPServer handler dispatch', () => {
       pathData: vi.fn(() => ({ from: 'a', to: 'b', found: false })),
     }));
 
-    const { startMCPServer } = await import('../../src/mcp.js');
+    const { startMCPServer } = await import('../../src/mcp/index.js');
     await startMCPServer('/tmp/test.db');
 
     const result = await handlers['tools/call']({
@@ -1033,7 +1033,7 @@ describe('startMCPServer handler dispatch', () => {
       ListToolsRequestSchema: 'tools/list',
       CallToolRequestSchema: 'tools/call',
     }));
-    vi.doMock('../../src/queries.js', () => ({
+    vi.doMock('../../src/domain/queries.js', () => ({
       EVERY_SYMBOL_KIND: [],
       EVERY_EDGE_KIND: [],
       VALID_ROLES: [],
@@ -1054,7 +1054,7 @@ describe('startMCPServer handler dispatch', () => {
       pathData: vi.fn(() => ({ from: 'a', to: 'b', found: false })),
     }));
 
-    const { startMCPServer } = await import('../../src/mcp.js');
+    const { startMCPServer } = await import('../../src/mcp/index.js');
     await startMCPServer('/tmp/test.db');
 
     const toolsList = await handlers['tools/list']();
@@ -1084,7 +1084,7 @@ describe('startMCPServer handler dispatch', () => {
       CallToolRequestSchema: 'tools/call',
     }));
 
-    vi.doMock('../../src/queries.js', () => ({
+    vi.doMock('../../src/domain/queries.js', () => ({
       EVERY_SYMBOL_KIND: [],
       EVERY_EDGE_KIND: [],
       VALID_ROLES: [],
@@ -1110,11 +1110,11 @@ describe('startMCPServer handler dispatch', () => {
       summary: { analyzed: 1, avgCognitive: 50, avgCyclomatic: 20 },
       thresholds: { cognitive: { warn: 15 }, cyclomatic: { warn: 10 }, maxNesting: { warn: 4 } },
     }));
-    vi.doMock('../../src/complexity.js', () => ({
+    vi.doMock('../../src/features/complexity.js', () => ({
       complexityData: complexityMock,
     }));
 
-    const { startMCPServer } = await import('../../src/mcp.js');
+    const { startMCPServer } = await import('../../src/mcp/index.js');
     await startMCPServer('/tmp/test.db');
 
     const result = await handlers['tools/call']({
diff --git a/tests/unit/normalize-symbol.test.js b/tests/unit/normalize-symbol.test.js
index 8a27b344..e6ec00cf 100644
--- a/tests/unit/normalize-symbol.test.js
+++ b/tests/unit/normalize-symbol.test.js
@@ -1,5 +1,5 @@
 import { describe, expect, test, vi } from 'vitest';
-import { normalizeSymbol } from '../../src/queries.js';
+import { normalizeSymbol } from '../../src/domain/queries.js';
 
 describe('normalizeSymbol', () => {
   test('full row with all fields', () => {
diff --git a/tests/unit/owners.test.js b/tests/unit/owners.test.js
index 40d4b361..52ed123c 100644
--- a/tests/unit/owners.test.js
+++ b/tests/unit/owners.test.js
@@ -8,7 +8,7 @@ import {
   parseCodeowners,
   parseCodeownersContent,
   patternToRegex,
-} from '../../src/owners.js';
+} from '../../src/features/owners.js';
 
 // ─── parseCodeownersContent ──────────────────────────────────────────
 
diff --git a/tests/unit/prompt-install.test.js b/tests/unit/prompt-install.test.js
index f23a73f8..d7e09981 100644
--- a/tests/unit/prompt-install.test.js
+++ b/tests/unit/prompt-install.test.js
@@ -44,7 +44,7 @@ describe('loadTransformers install prompt', () => {
       throw new Error('Cannot find package');
     });
 
-    const { embed } = await import('../../src/embeddings/index.js');
+    const { embed } = await import('../../src/domain/search/index.js');
 
     await expect(embed(['test'], 'minilm')).rejects.toThrow(
       'Semantic search requires @huggingface/transformers',
@@ -71,7 +71,7 @@ describe('loadTransformers install prompt', () => {
       throw new Error('Cannot find package');
     });
 
-    const { embed } = await import('../../src/embeddings/index.js');
+    const { embed } = await import('../../src/domain/search/index.js');
 
     await expect(embed(['test'], 'minilm')).rejects.toThrow(
       'Semantic search requires @huggingface/transformers',
@@ -99,7 +99,7 @@ describe('loadTransformers install prompt', () => {
       throw new Error('Cannot find package');
     });
 
-    const { embed } = await import('../../src/embeddings/index.js');
+    const { embed } = await import('../../src/domain/search/index.js');
 
     await expect(embed(['test'], 'minilm')).rejects.toThrow(
       'Semantic search requires @huggingface/transformers',
@@ -137,7 +137,7 @@ describe('loadTransformers install prompt', () => {
       };
     });
 
-    const { embed } = await import('../../src/embeddings/index.js');
+    const { embed } = await import('../../src/domain/search/index.js');
 
     const result = await embed(['test text'], 'minilm');
     expect(result.vectors).toHaveLength(1);
diff --git a/tests/unit/purge-files.test.js b/tests/unit/purge-files.test.js
index 9702899a..3e7ca8b5 100644
--- a/tests/unit/purge-files.test.js
+++ b/tests/unit/purge-files.test.js
@@ -7,8 +7,8 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterEach, describe, expect, test } from 'vitest';
-import { purgeFilesFromGraph } from '../../src/builder.js';
-import { initSchema } from '../../src/db.js';
+import { initSchema } from '../../src/db/index.js';
+import { purgeFilesFromGraph } from '../../src/domain/graph/builder.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/unit/queries-unit.test.js b/tests/unit/queries-unit.test.js
index db188420..19a6b2aa 100644
--- a/tests/unit/queries-unit.test.js
+++ b/tests/unit/queries-unit.test.js
@@ -14,8 +14,13 @@ import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
 import { afterAll, beforeAll, describe, expect, it, vi } from 'vitest';
-import { initSchema } from '../../src/db.js';
-import { diffImpactData, diffImpactMermaid, fnDepsData, fnImpactData } from '../../src/queries.js';
+import { initSchema } from '../../src/db/index.js';
+import {
+  diffImpactData,
+  diffImpactMermaid,
+  fnDepsData,
+  fnImpactData,
+} from '../../src/domain/queries.js';
 import {
   diffImpact,
   fileDeps,
@@ -23,7 +28,7 @@ import {
   fnImpact,
   impactAnalysis,
   moduleMap,
-} from '../../src/queries-cli.js';
+} from '../../src/presentation/queries-cli.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
diff --git a/tests/unit/resolve.test.js b/tests/unit/resolve.test.js
index 151322f4..d5e487b6 100644
--- a/tests/unit/resolve.test.js
+++ b/tests/unit/resolve.test.js
@@ -14,7 +14,7 @@ import {
   convertAliasesForNative,
   resolveImportPathJS,
   resolveImportsBatch,
-} from '../../src/resolve.js';
+} from '../../src/domain/graph/resolve.js';
 
 // ─── Temp project setup ──────────────────────────────────────────────
 
diff --git a/tests/unit/roles.test.js b/tests/unit/roles.test.js
index 5f8c0e1a..b703f899 100644
--- a/tests/unit/roles.test.js
+++ b/tests/unit/roles.test.js
@@ -15,8 +15,8 @@
 
 import Database from 'better-sqlite3';
 import { beforeEach, describe, expect, it } from 'vitest';
-import { initSchema } from '../../src/db.js';
-import { classifyNodeRoles } from '../../src/structure.js';
+import { initSchema } from '../../src/db/index.js';
+import { classifyNodeRoles } from '../../src/features/structure.js';
 
 let db;
 
diff --git a/tests/unit/snapshot.test.js b/tests/unit/snapshot.test.js
index 950028f1..b12b912a 100644
--- a/tests/unit/snapshot.test.js
+++ b/tests/unit/snapshot.test.js
@@ -10,7 +10,7 @@ import {
   snapshotSave,
   snapshotsDir,
   validateSnapshotName,
-} from '../../src/snapshot.js';
+} from '../../src/features/snapshot.js';
 
 let tmpDir;
 let dbPath;
diff --git a/tests/unit/structure.test.js b/tests/unit/structure.test.js
index 003a879d..fd57e487 100644
--- a/tests/unit/structure.test.js
+++ b/tests/unit/structure.test.js
@@ -7,8 +7,8 @@
 
 import Database from 'better-sqlite3';
 import { beforeEach, describe, expect, it } from 'vitest';
-import { initSchema } from '../../src/db.js';
-import { buildStructure } from '../../src/structure.js';
+import { initSchema } from '../../src/db/index.js';
+import { buildStructure } from '../../src/features/structure.js';
 
 let db;