@optave/codegraph 3.1.4 → 3.1.5

package/README.md

@@ -477,6 +477,8 @@ codegraph registry remove <name>  # Unregister
 | `-f, --file <path>` | Scope to a specific file (`fn`, `context`, `where`) |
 | `--mode <mode>` | Search mode: `hybrid` (default), `semantic`, or `keyword` (`search`) |
 | `--ndjson` | Output as newline-delimited JSON (one object per line) |
+| `--table` | Output as auto-column aligned table |
+| `--csv` | Output as CSV (RFC 4180, nested objects flattened) |
 | `--limit <n>` | Limit number of results |
 | `--offset <n>` | Skip first N results (pagination) |
 | `--rrf-k <n>` | RRF smoothing constant for multi-query search (default 60) |
@@ -560,14 +562,14 @@ Self-measured on every release via CI ([build benchmarks](generated/benchmarks/B
 
 | Metric | Latest |
 |---|---|
-| Build speed (native) | **5.1 ms/file** |
-| Build speed (WASM) | **14.6 ms/file** |
-| Query time | **4ms** |
-| No-op rebuild (native) | **6ms** |
-| 1-file rebuild (native) | **282ms** |
+| Build speed (native) | **3.5 ms/file** |
+| Build speed (WASM) | **9.6 ms/file** |
+| Query time | **3ms** |
+| No-op rebuild (native) | **9ms** |
+| 1-file rebuild (native) | **265ms** |
 | Query: fn-deps | **0.9ms** |
-| Query: path | **0.8ms** |
-| ~50,000 files (est.) | **~255.0s build** |
+| Query: path | **0.9ms** |
+| ~50,000 files (est.) | **~175.0s build** |
 
 Metrics are normalized per file for cross-version comparability. Times above are for a full initial build — incremental rebuilds only re-parse changed files.
 
@@ -603,16 +605,16 @@ codegraph mcp --repos a,b      # Restrict to specific repos (implies --multi-rep
 
 ### CLAUDE.md / Agent Instructions
 
-Add this to your project's `CLAUDE.md` to help AI agents use codegraph (full template in the [AI Agent Guide](docs/guides/ai-agent-guide.md#claudemd-template)):
+Add this to your project's `CLAUDE.md` to help AI agents use codegraph. Full template with all commands in the [AI Agent Guide](docs/guides/ai-agent-guide.md#claudemd-template).
 
 ```markdown
-## Code Navigation
+## Codegraph
 
-This project uses codegraph. The database is at `.codegraph/graph.db`.
+This project uses codegraph for dependency analysis. The graph is at `.codegraph/graph.db`.
 
-### Before modifying code, always:
+### Before modifying code:
 1. `codegraph where <name>` — find where the symbol lives
-2. `codegraph audit <file-or-function> --quick` — understand the structure
+2. `codegraph audit --quick <target>` — understand the structure
 3. `codegraph context <name> -T` — get full context (source, deps, callers)
 4. `codegraph fn-impact <name> -T` — check blast radius before editing
 
@@ -620,65 +622,19 @@ This project uses codegraph. The database is at `.codegraph/graph.db`.
 5. `codegraph diff-impact --staged -T` — verify impact before committing
 
 ### Other useful commands
-- `codegraph build .` — rebuild the graph (incremental by default)
-- `codegraph map` — module overview
-- `codegraph query <name> -T` — function call chain (callers + callees)
-- `codegraph path <from> <to> -T` — shortest call path between two symbols
-- `codegraph deps <file>` — file-level dependencies
-- `codegraph roles --role dead -T` — find dead code (unreferenced symbols)
-- `codegraph roles --role core -T` — find core symbols (high fan-in)
-- `codegraph co-change <file>` — files that historically change together
-- `codegraph complexity -T` — per-function complexity metrics (cognitive, cyclomatic, MI)
-- `codegraph communities --drift -T` — module boundary drift analysis
-- `codegraph check -T` — pass/fail rule check (CI gate, exit code 1 on fail)
-- `codegraph audit <target> -T` — combined structural summary + impact + health in one report
-- `codegraph triage -T` — ranked audit priority queue
-- `codegraph triage --level file -T` — file-level hotspot analysis
-- `codegraph check --staged` — CI validation predicates (exit code 0/1)
-- `codegraph batch target1 target2` — batch query multiple targets at once
-- `codegraph owners [target]` — CODEOWNERS mapping for symbols
-- `codegraph snapshot save <name>` — checkpoint the graph DB before refactoring
-- `codegraph branch-compare main HEAD -T` — structural diff between two refs (added/removed/changed symbols)
-- `codegraph exports <file>` — per-symbol consumer analysis (who calls each export)
-- `codegraph children <name>` — list parameters, properties, constants of a symbol
-- `codegraph dataflow <name>` — data flow edges (flows_to, returns, mutates)
-- `codegraph cfg <name>` — intraprocedural control flow graph
-- `codegraph ast <pattern>` — search stored AST nodes (calls, new, string, regex, throw, await)
-- `codegraph plot` — interactive HTML dependency graph viewer
-- `codegraph search "<query>"` — hybrid search (requires `codegraph embed`)
-- `codegraph search "<query>" --mode keyword` — BM25 keyword search
-- `codegraph cycles` — check for circular dependencies
+- `codegraph build .` — rebuild graph (incremental by default)
+- `codegraph map` — module overview · `codegraph stats` — graph health
+- `codegraph query <name> -T` — call chain · `codegraph path <from> <to> -T` — shortest path
+- `codegraph deps <file>` — file deps · `codegraph exports <file> -T` — export consumers
+- `codegraph audit <target> -T` — full risk report · `codegraph triage -T` — priority queue
+- `codegraph check --staged` — CI gate · `codegraph batch t1 t2 -T --json` — batch query
+- `codegraph search "<query>"` — semantic search · `codegraph cycles` — cycle detection
+- `codegraph roles --role dead -T` — dead code · `codegraph complexity -T` — metrics
+- `codegraph dataflow <name> -T` — data flow · `codegraph cfg <name> -T` — control flow
 
 ### Flags
-- `-T` / `--no-tests` — exclude test files (use by default)
-- `-j` / `--json` — JSON output for programmatic use
-- `-f, --file <path>` — scope to a specific file
-- `-k, --kind <kind>` — filter by symbol kind
-
-### Semantic search
-
-Use `codegraph search` to find functions by intent rather than exact name.
-When a single query might miss results, combine multiple angles with `;`:
-
-  codegraph search "validate auth; check token; verify JWT"
-  codegraph search "parse config; load settings" --kind function
-
-Multi-query search uses Reciprocal Rank Fusion — functions that rank
-highly across several queries surface first. This is especially useful
-when you're not sure what naming convention the codebase uses.
-
-When writing multi-queries, use 2-4 sub-queries (2-4 words each) that
-attack the problem from different angles. Pick from these strategies:
-- **Naming variants**: cover synonyms the author might have used
-  ("send email; notify user; deliver message")
-- **Abstraction levels**: pair high-level intent with low-level operation
-  ("handle payment; charge credit card")
-- **Input/output sides**: cover the read half and write half
-  ("parse config; apply settings")
-- **Domain + technical**: bridge business language and implementation
-  ("onboard tenant; create organization; provision workspace")
-
-Use `--kind function` to cut noise. Use `--file <pattern>` to scope.
+- `-T` — exclude test files (use by default) · `-j` — JSON output
+- `-f, --file <path>` — scope to file · `-k, --kind <kind>` — filter kind
 ```
 
 ## 📋 Recommended Practices
@@ -821,7 +777,7 @@ See **[ROADMAP.md](docs/roadmap/ROADMAP.md)** for the full development roadmap a
 1. ~~**Rust Core**~~ — **Complete** (v1.3.0) — native tree-sitter parsing via napi-rs, parallel multi-core parsing, incremental re-parsing, import resolution & cycle detection in Rust
 2. ~~**Foundation Hardening**~~ — **Complete** (v1.4.0) — parser registry, 12-tool MCP server with multi-repo support, test coverage 62%→75%, `apiKeyCommand` secret resolution, global repo registry
 3. ~~**Deep Analysis**~~ — **Complete** (v3.0.0) — dataflow analysis (flows_to, returns, mutates), intraprocedural CFG for all 11 languages, stored AST nodes, expanded node/edge types (parameter, property, constant, contains, parameter_of, receiver), GraphML/GraphSON/Neo4j CSV export, interactive HTML viewer, CLI consolidation, stable JSON schema
-4. **Architectural Refactoring** — **In Progress** (v3.1.4) — unified AST analysis, composable MCP, domain errors, builder pipeline, embedder subsystem, graph model, qualified names, presentation layer, InMemoryRepository (11/14 tasks complete)
+4. ~~**Architectural Refactoring**~~ — **Complete** (v3.1.5) — unified AST analysis, composable MCP, domain errors, builder pipeline, embedder subsystem, graph model, qualified names, presentation layer, InMemoryRepository, domain directory grouping, CLI composability
 5. **Natural Language Queries** — `codegraph ask` command, conversational sessions
 6. **Expanded Language Support** — 8 new languages (12 → 20)
 7. **GitHub Integration & CI** — reusable GitHub Action, PR review, SARIF output

package/package.json

@@ -1,12 +1,14 @@
 {
   "name": "@optave/codegraph",
-  "version": "3.1.4",
+  "version": "3.1.5",
   "description": "Local code graph CLI — parse codebases with tree-sitter, build dependency graphs, query them",
   "type": "module",
   "main": "src/index.js",
   "exports": {
     ".": {
-      "import": "./src/index.js"
+      "import": "./src/index.js",
+      "require": "./src/index.cjs",
+      "default": "./src/index.cjs"
     },
     "./cli": {
       "import": "./src/cli.js"
@@ -74,12 +76,12 @@
   },
   "optionalDependencies": {
     "@modelcontextprotocol/sdk": "^1.0.0",
-    "@optave/codegraph-darwin-arm64": "3.1.4",
-    "@optave/codegraph-darwin-x64": "3.1.4",
-    "@optave/codegraph-linux-arm64-gnu": "3.1.4",
-    "@optave/codegraph-linux-x64-gnu": "3.1.4",
-    "@optave/codegraph-linux-x64-musl": "3.1.4",
-    "@optave/codegraph-win32-x64-msvc": "3.1.4"
+    "@optave/codegraph-darwin-arm64": "3.1.5",
+    "@optave/codegraph-darwin-x64": "3.1.5",
+    "@optave/codegraph-linux-arm64-gnu": "3.1.5",
+    "@optave/codegraph-linux-x64-gnu": "3.1.5",
+    "@optave/codegraph-linux-x64-musl": "3.1.5",
+    "@optave/codegraph-win32-x64-msvc": "3.1.5"
   },
   "devDependencies": {
     "@biomejs/biome": "^2.4.4",

package/src/ast-analysis/engine.js

@@ -17,8 +17,8 @@
 
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
-import { bulkNodeIdsByFile } from '../db.js';
-import { debug } from '../logger.js';
+import { bulkNodeIdsByFile } from '../db/index.js';
+import { debug } from '../infrastructure/logger.js';
 import { computeLOCMetrics, computeMaintainabilityIndex } from './metrics.js';
 import {
   AST_TYPE_MAPS,
@@ -38,6 +38,7 @@ import { createDataflowVisitor } from './visitors/dataflow-visitor.js';
 // ─── Extension sets for quick language-support checks ────────────────────
 
 const CFG_EXTENSIONS = buildExtensionSet(CFG_RULES);
+const COMPLEXITY_EXTENSIONS = buildExtensionSet(COMPLEXITY_RULES);
 const DATAFLOW_EXTENSIONS = buildExtensionSet(DATAFLOW_RULES);
 const WALK_EXTENSIONS = buildExtensionSet(AST_TYPE_MAPS);
 
@@ -45,7 +46,7 @@ const WALK_EXTENSIONS = buildExtensionSet(AST_TYPE_MAPS);
 
 let _parserModule = null;
 async function getParserModule() {
-  if (!_parserModule) _parserModule = await import('../parser.js');
+  if (!_parserModule) _parserModule = await import('../domain/parser.js');
   return _parserModule;
 }
 
@@ -74,15 +75,34 @@ export async function runAnalyses(db, fileSymbols, rootDir, opts, engineOpts) {
   const extToLang = buildExtToLangMap();
 
   // ── WASM pre-parse for files that need it ───────────────────────────
-  // CFG now runs as a visitor in the unified walk, so only dataflow
-  // triggers WASM pre-parse when no tree exists.
-  if (doDataflow) {
+  // The native engine only handles parsing (symbols, calls, imports).
+  // Complexity, CFG, and dataflow all require a WASM tree-sitter tree
+  // for their visitor walks. Without this, incremental rebuilds on the
+  // native engine silently lose these analyses for changed files (#468).
+  if (doComplexity || doCfg || doDataflow) {
     let needsWasmTrees = false;
     for (const [relPath, symbols] of fileSymbols) {
       if (symbols._tree) continue;
       const ext = path.extname(relPath).toLowerCase();
-
-      if (!symbols.dataflow && DATAFLOW_EXTENSIONS.has(ext)) {
+      const defs = symbols.definitions || [];
+
+      const needsComplexity =
+        doComplexity &&
+        COMPLEXITY_EXTENSIONS.has(ext) &&
+        defs.some((d) => (d.kind === 'function' || d.kind === 'method') && d.line && !d.complexity);
+      const needsCfg =
+        doCfg &&
+        CFG_EXTENSIONS.has(ext) &&
+        defs.some(
+          (d) =>
+            (d.kind === 'function' || d.kind === 'method') &&
+            d.line &&
+            d.cfg !== null &&
+            !Array.isArray(d.cfg?.blocks),
+        );
+      const needsDataflow = doDataflow && !symbols.dataflow && DATAFLOW_EXTENSIONS.has(ext);
+
+      if (needsComplexity || needsCfg || needsDataflow) {
         needsWasmTrees = true;
         break;
       }
@@ -320,7 +340,7 @@ export async function runAnalyses(db, fileSymbols, rootDir, opts, engineOpts) {
   if (doAst) {
     const t0 = performance.now();
     try {
-      const { buildAstNodes } = await import('../ast.js');
+      const { buildAstNodes } = await import('../features/ast.js');
       await buildAstNodes(db, fileSymbols, rootDir, engineOpts);
     } catch (err) {
       debug(`buildAstNodes failed: ${err.message}`);
@@ -331,7 +351,7 @@ export async function runAnalyses(db, fileSymbols, rootDir, opts, engineOpts) {
   if (doComplexity) {
     const t0 = performance.now();
     try {
-      const { buildComplexityMetrics } = await import('../complexity.js');
+      const { buildComplexityMetrics } = await import('../features/complexity.js');
       await buildComplexityMetrics(db, fileSymbols, rootDir, engineOpts);
     } catch (err) {
       debug(`buildComplexityMetrics failed: ${err.message}`);
@@ -342,7 +362,7 @@ export async function runAnalyses(db, fileSymbols, rootDir, opts, engineOpts) {
   if (doCfg) {
     const t0 = performance.now();
     try {
-      const { buildCFGData } = await import('../cfg.js');
+      const { buildCFGData } = await import('../features/cfg.js');
       await buildCFGData(db, fileSymbols, rootDir, engineOpts);
     } catch (err) {
       debug(`buildCFGData failed: ${err.message}`);
@@ -353,7 +373,7 @@ export async function runAnalyses(db, fileSymbols, rootDir, opts, engineOpts) {
   if (doDataflow) {
     const t0 = performance.now();
     try {
-      const { buildDataflowEdges } = await import('../dataflow.js');
+      const { buildDataflowEdges } = await import('../features/dataflow.js');
       await buildDataflowEdges(db, fileSymbols, rootDir, engineOpts);
     } catch (err) {
       debug(`buildDataflowEdges failed: ${err.message}`);

package/src/ast-analysis/shared.js

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

package/src/cli/commands/ast.js

@@ -1,4 +1,4 @@
-import { ConfigError } from '../../errors.js';
+import { ConfigError } from '../../shared/errors.js';
 
 export const command = {
   name: 'ast [pattern]',
@@ -16,11 +16,7 @@ export const command = {
     astQuery(pattern, opts.db, {
       kind: opts.kind,
       file: opts.file,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
-      ndjson: opts.ndjson,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/audit.js

@@ -1,6 +1,7 @@
-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 { audit } from '../../presentation/audit.js';
+import { explain } from '../../presentation/queries-cli.js';
+import { config } from '../shared/options.js';
 
 export const command = {
   name: 'audit <target>',
@@ -24,14 +25,11 @@ export const command = {
     }
   },
   execute([target], opts, ctx) {
+    const qOpts = ctx.resolveQueryOpts(opts);
     if (opts.quick) {
       explain(target, opts.db, {
         depth: parseInt(opts.depth, 10),
-        noTests: ctx.resolveNoTests(opts),
-        json: opts.json,
-        limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-        offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-        ndjson: opts.ndjson,
+        ...qOpts,
       });
       return;
     }
@@ -39,8 +37,9 @@ export const command = {
       depth: parseInt(opts.depth, 10),
       file: opts.file,
       kind: opts.kind,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
+      noTests: qOpts.noTests,
+      json: qOpts.json,
+      config,
     });
   },
 };

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

package/src/cli/commands/branch-compare.js

@@ -9,7 +9,7 @@ export const command = {
     ['-f, --format <format>', 'Output format: text, mermaid, json', 'text'],
   ],
   async execute([base, target], opts, ctx) {
-    const { branchCompare } = await import('../../commands/branch-compare.js');
+    const { branchCompare } = await import('../../presentation/branch-compare.js');
     await branchCompare(base, target, {
       engine: ctx.program.opts().engine,
       depth: parseInt(opts.depth, 10),

package/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]',

package/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>',
@@ -15,16 +15,12 @@ export const command = {
     }
   },
   async execute([name], opts, ctx) {
-    const { cfg } = await import('../../commands/cfg.js');
+    const { cfg } = await import('../../presentation/cfg.js');
     cfg(name, opts.db, {
       format: opts.format,
       file: opts.file,
       kind: opts.kind,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
-      ndjson: opts.ndjson,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/check.js

@@ -1,5 +1,6 @@
-import { ConfigError } from '../../errors.js';
-import { EVERY_SYMBOL_KIND } from '../../queries.js';
+import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
+import { ConfigError } from '../../shared/errors.js';
+import { config } from '../shared/options.js';
 
 export const command = {
   name: 'check [ref]',
@@ -25,6 +26,7 @@ export const command = {
   ],
   async execute([ref], opts, ctx) {
     const isDiffMode = ref || opts.staged;
+    const qOpts = ctx.resolveQueryOpts(opts);
 
     if (!isDiffMode && !opts.rules) {
       if (opts.kind && !EVERY_SYMBOL_KIND.includes(opts.kind)) {
@@ -32,20 +34,16 @@ export const command = {
           `Invalid kind "${opts.kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`,
         );
       }
-      const { manifesto } = await import('../../commands/manifesto.js');
+      const { manifesto } = await import('../../presentation/manifesto.js');
       manifesto(opts.db, {
         file: opts.file,
         kind: opts.kind,
-        noTests: ctx.resolveNoTests(opts),
-        json: opts.json,
-        limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-        offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-        ndjson: opts.ndjson,
+        ...qOpts,
       });
       return;
     }
 
-    const { check } = await import('../../commands/check.js');
+    const { check } = await import('../../presentation/check.js');
     check(opts.db, {
       ref,
       staged: opts.staged,
@@ -54,8 +52,9 @@ export const command = {
       signatures: opts.signatures || undefined,
       boundaries: opts.boundaries || undefined,
       depth: opts.depth ? parseInt(opts.depth, 10) : undefined,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
+      noTests: qOpts.noTests,
+      json: qOpts.json,
+      config,
     });
 
     if (opts.rules) {
@@ -64,15 +63,11 @@ export const command = {
           `Invalid kind "${opts.kind}". Valid: ${EVERY_SYMBOL_KIND.join(', ')}`,
         );
       }
-      const { manifesto } = await import('../../commands/manifesto.js');
+      const { manifesto } = await import('../../presentation/manifesto.js');
       manifesto(opts.db, {
         file: opts.file,
         kind: opts.kind,
-        noTests: ctx.resolveNoTests(opts),
-        json: opts.json,
-        limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-        offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-        ndjson: opts.ndjson,
+        ...qOpts,
       });
     }
   },

package/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>',
@@ -22,10 +22,7 @@ export const command = {
     children(name, opts.db, {
       file: opts.file,
       kind: opts.kind,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/co-change.js

@@ -1,4 +1,4 @@
-import { AnalysisError } from '../../errors.js';
+import { AnalysisError } from '../../shared/errors.js';
 
 export const command = {
   name: 'co-change [file]',
@@ -19,8 +19,10 @@ export const command = {
     ['--ndjson', 'Newline-delimited JSON output'],
   ],
   async execute([file], opts, ctx) {
-    const { analyzeCoChanges, coChangeData, coChangeTopData } = await import('../../cochange.js');
-    const { formatCoChange, formatCoChangeTop } = await import('../../commands/cochange.js');
+    const { analyzeCoChanges, coChangeData, coChangeTopData } = await import(
+      '../../features/cochange.js'
+    );
+    const { formatCoChange, formatCoChangeTop } = await import('../../presentation/cochange.js');
 
     if (opts.analyze) {
       const result = analyzeCoChanges(opts.db, {

package/src/cli/commands/communities.js

@@ -8,16 +8,12 @@ export const command = {
     ['--drift', 'Show only drift analysis'],
   ],
   async execute(_args, opts, ctx) {
-    const { communities } = await import('../../commands/communities.js');
+    const { communities } = await import('../../presentation/communities.js');
     communities(opts.db, {
       functions: opts.functions,
       resolution: parseFloat(opts.resolution),
       drift: opts.drift,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      ndjson: opts.ndjson,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/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]',
@@ -27,7 +27,7 @@ export const command = {
     }
   },
   async execute([target], opts, ctx) {
-    const { complexity } = await import('../../commands/complexity.js');
+    const { complexity } = await import('../../presentation/complexity.js');
     complexity(opts.db, {
       target,
       limit: parseInt(opts.limit, 10),
@@ -40,6 +40,7 @@ export const command = {
       noTests: ctx.resolveNoTests(opts),
       json: opts.json,
       ndjson: opts.ndjson,
+      config: ctx.config,
     });
   },
 };

package/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>',
@@ -23,12 +23,8 @@ export const command = {
       file: opts.file,
       kind: opts.kind,
       noSource: !opts.source,
-      noTests: ctx.resolveNoTests(opts),
       includeTests: opts.withTestSource,
-      json: opts.json,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
-      ndjson: opts.ndjson,
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };

package/src/cli/commands/cycles.js

@@ -1,5 +1,5 @@
-import { findCycles, formatCycles } from '../../cycles.js';
-import { openReadonlyOrFail } from '../../db.js';
+import { findCycles, formatCycles } from '../../domain/graph/cycles.js';
+import { openGraph } from '../shared/open-graph.js';
 
 export const command = {
   name: 'cycles',
@@ -12,12 +12,16 @@ export const command = {
     ['-j, --json', 'Output as JSON'],
   ],
   execute(_args, opts, ctx) {
-    const db = openReadonlyOrFail(opts.db);
-    const cycles = findCycles(db, {
-      fileLevel: !opts.functions,
-      noTests: ctx.resolveNoTests(opts),
-    });
-    db.close();
+    const { db, close } = openGraph(opts);
+    let cycles;
+    try {
+      cycles = findCycles(db, {
+        fileLevel: !opts.functions,
+        noTests: ctx.resolveNoTests(opts),
+      });
+    } finally {
+      close();
+    }
 
     if (opts.json) {
       console.log(JSON.stringify({ cycles, count: cycles.length }, null, 2));

package/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>',
@@ -16,17 +16,13 @@ export const command = {
     }
   },
   async execute([name], opts, ctx) {
-    const { dataflow } = await import('../../commands/dataflow.js');
+    const { dataflow } = await import('../../presentation/dataflow.js');
     dataflow(name, opts.db, {
       file: opts.file,
       kind: opts.kind,
-      noTests: ctx.resolveNoTests(opts),
-      json: opts.json,
-      ndjson: opts.ndjson,
-      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
-      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
       impact: opts.impact,
       depth: parseInt(opts.depth, 10),
+      ...ctx.resolveQueryOpts(opts),
     });
   },
 };