refactor: resolve three architecture issues after #456 and #458

CLAUDE.md

@@ -123,8 +123,14 @@ JS source is plain JavaScript (ES modules) in `src/`. No transpilation step. The
 | `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) |
+| `features/graph-enrichment.js` | Data enrichment for HTML viewer (complexity, communities, fan-in/out) |
+| **`presentation/`** | **Pure output formatting + CLI command wrappers** |
+| `presentation/viewer.js` | Interactive HTML renderer with vis-network |
+| `presentation/queries-cli/` | CLI display wrappers for query functions, split by concern: `path.js`, `overview.js`, `inspect.js`, `impact.js`, `exports.js` |
+| `presentation/*.js` | Command formatters (audit, batch, check, communities, complexity, etc.) — call `features/*.js`, format output, set exit codes |
+| `presentation/export.js` | DOT/Mermaid/GraphML/Neo4j serializers |
+| `presentation/sequence-renderer.js` | Mermaid sequence diagram rendering |
+| `presentation/table.js`, `result-formatter.js`, `colors.js` | CLI table formatting, JSON/NDJSON output, color constants |
 | **`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** |

src/cli/commands/audit.js

@@ -1,5 +1,5 @@
-import { audit } from '../../commands/audit.js';
 import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
+import { audit } from '../../presentation/audit.js';
 import { explain } from '../../presentation/queries-cli.js';
 
 export const command = {

src/cli/commands/batch.js

@@ -1,7 +1,7 @@
 import fs from 'node:fs';
-import { batch } from '../../commands/batch.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 = {

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),

src/cli/commands/cfg.js

@@ -15,7 +15,7 @@ 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,

src/cli/commands/check.js

@@ -32,7 +32,7 @@ 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,
@@ -45,7 +45,7 @@ export const command = {
       return;
     }
 
-    const { check } = await import('../../commands/check.js');
+    const { check } = await import('../../presentation/check.js');
     check(opts.db, {
       ref,
       staged: opts.staged,
@@ -64,7 +64,7 @@ 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,

src/cli/commands/co-change.js

@@ -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, {

src/cli/commands/communities.js

@@ -8,7 +8,7 @@ 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),

src/cli/commands/complexity.js

@@ -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),

src/cli/commands/dataflow.js

@@ -16,7 +16,7 @@ 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,

src/cli/commands/flow.js

@@ -20,7 +20,7 @@ export const command = {
     }
   },
   async execute([name], opts, ctx) {
-    const { flow } = await import('../../commands/flow.js');
+    const { flow } = await import('../../presentation/flow.js');
     flow(name, opts.db, {
       list: opts.list,
       depth: parseInt(opts.depth, 10),

src/cli/commands/owners.js

@@ -12,7 +12,7 @@ export const command = {
     ['-j, --json', 'Output as JSON'],
   ],
   async execute([target], opts, ctx) {
-    const { owners } = await import('../../commands/owners.js');
+    const { owners } = await import('../../presentation/owners.js');
     owners(opts.db, {
       owner: opts.owner,
       boundary: opts.boundary,

src/cli/commands/plot.js

@@ -22,7 +22,7 @@ export const command = {
     ['--color-by <mode>', 'Color nodes by: kind | role | community | complexity'],
   ],
   async execute(_args, opts, ctx) {
-    const { generatePlotHTML, loadPlotConfig } = await import('../../viewer.js');
+    const { generatePlotHTML, loadPlotConfig } = await import('../../features/graph-enrichment.js');
     const os = await import('node:os');
     const db = openReadonlyOrFail(opts.db);
 

src/cli/commands/sequence.js

@@ -16,7 +16,7 @@ export const command = {
     }
   },
   async execute([name], opts, ctx) {
-    const { sequence } = await import('../../commands/sequence.js');
+    const { sequence } = await import('../../presentation/sequence.js');
     sequence(name, opts.db, {
       depth: parseInt(opts.depth, 10),
       file: opts.file,

src/cli/commands/structure.js

@@ -15,7 +15,7 @@ export const command = {
     ['--ndjson', 'Newline-delimited JSON output'],
   ],
   async execute([dir], opts, ctx) {
-    const { structureData, formatStructure } = await import('../../commands/structure.js');
+    const { structureData, formatStructure } = await import('../../presentation/structure.js');
     const data = structureData(opts.db, {
       directory: dir,
       depth: opts.depth ? parseInt(opts.depth, 10) : undefined,

src/cli/commands/triage.js

@@ -31,7 +31,7 @@ export const command = {
   ],
   async execute(_args, opts, ctx) {
     if (opts.level === 'file' || opts.level === 'directory') {
-      const { hotspotsData, formatHotspots } = await import('../../commands/structure.js');
+      const { hotspotsData, formatHotspots } = await import('../../presentation/structure.js');
       const metric = opts.sort === 'risk' ? 'fan-in' : opts.sort;
       const data = hotspotsData(opts.db, {
         metric,
@@ -60,7 +60,7 @@ export const command = {
         throw new ConfigError('Invalid --weights JSON', { cause: err });
       }
     }
-    const { triage } = await import('../../commands/triage.js');
+    const { triage } = await import('../../presentation/triage.js');
     triage(opts.db, {
       limit: parseInt(opts.limit, 10),
       offset: opts.offset ? parseInt(opts.offset, 10) : undefined,