test(mcp): add adapter-level tests for dependsOn and connected components

Cover the two untested graph feature paths: RefsAdapter dependsOn
(path tracing, hop count, no-path, missing indexer) and MapAdapter
connected components (multi-cluster subsystems, single-cluster skip).
Clean up stale scratchpad entries for already-wired features.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: prosdev

.claude/scratchpad.md

@@ -12,14 +12,11 @@
 ## Future Work
 
 - Antfly SDK: server-side path filter for `getDocsByFilePath` (eliminates 5k cap)
-- Wire `shortestPath` into `dev_refs` as a "trace path" feature (graph.ts is ready, adapter wiring is separate scope)
-- Wire `connectedComponents` into `dev_map` verbose output (graph.ts is ready)
 - Betweenness centrality — identifies bridge files between subsystems. Worth adding if agents need refactoring guidance. graphology (MIT, 1.6k stars) is the upgrade path if we need more than 3 hand-rolled algorithms.
 - **Connected components hub filtering** — widely-shared utility files (e.g., logger.ts imported by 50+ files) merge separate subsystems into one component. Filter out hub nodes (high in-degree) before computing components for better subsystem identification.
 - **PageRank at 10k+ nodes** — convergence tolerance 1e-6 may require all 100 iterations for large sparse graphs. Monitor performance. Consider reducing maxIterations or loosening tolerance for dev_map where approximate ranks are fine.
 - **getAll(limit: 10000) truncation** — medium-large monorepos may exceed 10k docs. Warning is logged but results are silently incomplete. Long-term: paginate or make limit configurable.
 - E2E tests in CI — blocked on Antfly memory requirements vs GitHub runner limits (7GB)
-- **Python language support** — plan written at `.claude/da-plans/core/phase-4-python-support/`. 4 parts: bundle WASM + queries, PythonScanner, pattern rules, test fixtures + docs.
 - Vue/Svelte SFC support — `.vue`/`.svelte` files have embedded `<script lang="ts">` blocks. Would need script block extraction before tree-sitter parsing. Lower priority — co-located `.ts` files in those projects already get full analysis.
 - Swap `WasmPatternMatcher` to `@ast-grep/napi` if bulk scanning perf becomes an issue (~4x faster native Rust). Interface is ready; implementation is mechanical.
 
@@ -29,12 +26,10 @@
 
 ## Test Gaps
 
-- **RefsAdapter integration test with `dependsOn`.** The `traceTo` path tracing feature is tested at the algorithm level (shortestPath in graph.test.ts) but not at the adapter level. Needs a test that constructs RefsAdapter with a mock indexer, calls `execute()` with `traceTo`, and verifies the path output format. Also needs a test for the error case when indexer is missing.
 - **InspectAdapter integration test with PatternMatcher.** The InspectAdapter test constructs without a `patternMatcher` — the AST path is never exercised through the MCP layer. Needs a test that constructs `InspectAdapter` with `createPatternMatcher()`, mocks the search service, calls `execute()`, and verifies AST-enhanced results flow through. Requires mock search service setup — larger integration test scope.
 
 ## Tech Debt
 
-- **`isTestFile()` is hardcoded for JS/TS and Go.** Only checks for `.test.`, `.spec.` (JS/TS) and `_test.go` (Go). Python needs `test_*.py`, `*_test.py`, `conftest.py`. Future languages will need their own patterns. Should be refactored to a language-aware registry or pattern map instead of growing if/else chains. Tracked in Phase 4 Part 4.2.
 
 ## Notes
 

packages/mcp-server/src/adapters/__tests__/map-adapter.test.ts

@@ -259,6 +259,122 @@ describe('MapAdapter', () => {
     });
   });
 
+  describe('Connected Components', () => {
+    it('should include subsystems when docs have call graph edges', async () => {
+      // Docs with callees forming two separate clusters
+      const clusterDocs: SearchResult[] = [
+        {
+          id: 'packages/core/src/a.ts:fnA:1',
+          score: 0.9,
+          metadata: {
+            path: 'packages/core/src/a.ts',
+            type: 'function',
+            name: 'fnA',
+            exported: true,
+            callees: [{ name: 'fnB', file: 'packages/core/src/b.ts', line: 1 }],
+          },
+        },
+        {
+          id: 'packages/core/src/b.ts:fnB:1',
+          score: 0.9,
+          metadata: {
+            path: 'packages/core/src/b.ts',
+            type: 'function',
+            name: 'fnB',
+            exported: true,
+            callees: [],
+          },
+        },
+        {
+          id: 'packages/mcp/src/x.ts:fnX:1',
+          score: 0.9,
+          metadata: {
+            path: 'packages/mcp/src/x.ts',
+            type: 'function',
+            name: 'fnX',
+            exported: true,
+            callees: [{ name: 'fnY', file: 'packages/mcp/src/y.ts', line: 1 }],
+          },
+        },
+        {
+          id: 'packages/mcp/src/y.ts:fnY:1',
+          score: 0.9,
+          metadata: {
+            path: 'packages/mcp/src/y.ts',
+            type: 'function',
+            name: 'fnY',
+            exported: true,
+            callees: [],
+          },
+        },
+      ];
+
+      const clusterIndexer = {
+        search: vi.fn().mockResolvedValue(clusterDocs),
+        getAll: vi.fn().mockResolvedValue(clusterDocs),
+      } as unknown as RepositoryIndexer;
+
+      const clusterAdapter = new MapAdapter({
+        repositoryIndexer: clusterIndexer,
+        defaultDepth: 3,
+        defaultTokenBudget: 5000,
+      });
+      await clusterAdapter.initialize(context);
+
+      const result = await clusterAdapter.execute({ depth: 3 }, execContext);
+
+      expect(result.success).toBe(true);
+      expect(result.data).toContain('Subsystems');
+      expect(result.data).toContain('connected');
+    });
+
+    it('should not show subsystems section when all docs are in one cluster', async () => {
+      // All docs in same cluster (single connected component)
+      const singleClusterDocs: SearchResult[] = [
+        {
+          id: 'src/a.ts:fnA:1',
+          score: 0.9,
+          metadata: {
+            path: 'src/a.ts',
+            type: 'function',
+            name: 'fnA',
+            exported: true,
+            callees: [{ name: 'fnB', file: 'src/b.ts', line: 1 }],
+          },
+        },
+        {
+          id: 'src/b.ts:fnB:1',
+          score: 0.9,
+          metadata: {
+            path: 'src/b.ts',
+            type: 'function',
+            name: 'fnB',
+            exported: true,
+            callees: [{ name: 'fnA', file: 'src/a.ts', line: 1 }],
+          },
+        },
+      ];
+
+      const singleIndexer = {
+        search: vi.fn().mockResolvedValue(singleClusterDocs),
+        getAll: vi.fn().mockResolvedValue(singleClusterDocs),
+      } as unknown as RepositoryIndexer;
+
+      const singleAdapter = new MapAdapter({
+        repositoryIndexer: singleIndexer,
+        defaultDepth: 2,
+        defaultTokenBudget: 5000,
+      });
+      await singleAdapter.initialize(context);
+
+      const result = await singleAdapter.execute({}, execContext);
+
+      expect(result.success).toBe(true);
+      // Only 1 component — formatCodebaseMap skips the section when <= 1
+      expect(result.data).not.toContain('Subsystems');
+    });
+  });
+
   describe('Token Estimation', () => {
     it('should estimate tokens based on depth', () => {
       const shallow = adapter.estimateTokens({ depth: 1 });

packages/mcp-server/src/adapters/__tests__/refs-adapter.test.ts

@@ -268,6 +268,98 @@ describe('RefsAdapter', () => {
     });
   });
 
+  describe('Dependency Path Tracing (dependsOn)', () => {
+    let adapterWithIndexer: RefsAdapter;
+
+    // Mock indexer that returns docs with callees forming a chain:
+    // src/planner.ts → src/github.ts → src/api.ts
+    const chainDocs: SearchResult[] = [
+      {
+        id: '1',
+        score: 0.9,
+        metadata: {
+          path: 'src/planner.ts',
+          callees: [{ name: 'fetchIssue', file: 'src/github.ts', line: 15 }],
+        },
+      },
+      {
+        id: '2',
+        score: 0.9,
+        metadata: {
+          path: 'src/github.ts',
+          callees: [{ name: 'httpGet', file: 'src/api.ts', line: 5 }],
+        },
+      },
+      {
+        id: '3',
+        score: 0.9,
+        metadata: {
+          path: 'src/api.ts',
+          callees: [],
+        },
+      },
+    ];
+
+    beforeEach(async () => {
+      const mockIndexer = {
+        getAll: vi.fn().mockResolvedValue(chainDocs),
+      };
+
+      adapterWithIndexer = new RefsAdapter({
+        searchService: mockSearchService,
+        indexer: mockIndexer as unknown as import('@prosdevlab/dev-agent-core').RepositoryIndexer,
+        defaultLimit: 20,
+      });
+
+      await adapterWithIndexer.initialize(context);
+    });
+
+    it('should trace dependency path between files', async () => {
+      const result = await adapterWithIndexer.execute(
+        { name: 'createPlan', dependsOn: 'src/api.ts' },
+        execContext
+      );
+
+      expect(result.success).toBe(true);
+      expect(result.data).toContain('Dependency Path');
+      expect(result.data).toContain('src/planner.ts');
+      expect(result.data).toContain('src/api.ts');
+      expect(result.data).toContain('→');
+    });
+
+    it('should report hop count', async () => {
+      const result = await adapterWithIndexer.execute(
+        { name: 'createPlan', dependsOn: 'src/api.ts' },
+        execContext
+      );
+
+      expect(result.success).toBe(true);
+      expect(result.data).toContain('2 hops');
+    });
+
+    it('should report when no path exists', async () => {
+      const result = await adapterWithIndexer.execute(
+        { name: 'createPlan', dependsOn: 'src/nonexistent.ts' },
+        execContext
+      );
+
+      expect(result.success).toBe(true);
+      expect(result.data).toContain('No Path Found');
+      expect(result.data).toContain('separate subsystems');
+    });
+
+    it('should return error when indexer is not available', async () => {
+      // The base adapter (no indexer) should fail for dependsOn
+      const result = await adapter.execute(
+        { name: 'createPlan', dependsOn: 'src/api.ts' },
+        execContext
+      );
+
+      expect(result.success).toBe(false);
+      expect(result.error?.code).toBe('INDEX_REQUIRED');
+    });
+  });
+
   describe('Not Found', () => {
     it('should return error when function not found', async () => {
       // Mock empty results