Improve test isolation and coverage for CLI and VS Code

.changeset/ci-diagnostics-symbol-refresh.md

@@ -0,0 +1,6 @@
+---
+"kibi-cli": patch
+"kibi-mcp": patch
+---
+
+Add CI-only diagnostic logging for symbol coordinate refresh to help isolate the refreshCoordinatesForSymbolId coverage failure on GitHub Actions.

.changeset/mcp-refresh-seam-isolation.md

@@ -0,0 +1,5 @@
+---
+"kibi-mcp": patch
+---
+
+Replace mock.module-based symbol refresh mocking in MCP upsert tests with a test seam to prevent cross-file leakages under coverage.

documentation/symbols.yaml

@@ -1,9 +1,9 @@
 # symbols.yaml
 # AUTHORED fields (edit freely):
 #   id, title, sourceFile, links, status, tags, owner, priority
-# GENERATED fields (never edit manually — overwritten by kibi sync and kb_symbols_refresh):
+# GENERATED fields (never edit manually — overwritten by kibi sync and kb.symbols.refresh):
 #   sourceLine, sourceColumn, sourceEndLine, sourceEndColumn, coordinatesGeneratedAt
-# Run `kibi sync` or call the `kb_symbols_refresh` MCP tool to refresh coordinates.
+# Run `kibi sync` or call the `kb.symbols.refresh` MCP tool to refresh coordinates.
 symbols:
   - id: SYM-001
     title: PrologProcess
@@ -20,7 +20,7 @@ symbols:
     sourceColumn: 13
     sourceEndLine: 576
     sourceEndColumn: 1
-    coordinatesGeneratedAt: '2026-03-28T18:53:57.173Z'
+    coordinatesGeneratedAt: '2026-03-31T09:19:46.625Z'
   - id: SYM-002
     title: handleKbUpsert
     sourceFile: packages/mcp/src/tools/upsert.ts
@@ -36,7 +36,7 @@ symbols:
     sourceColumn: 22
     sourceEndLine: 244
     sourceEndColumn: 1
-    coordinatesGeneratedAt: '2026-03-28T18:53:57.274Z'
+    coordinatesGeneratedAt: '2026-03-31T09:19:46.728Z'
   - id: SYM-003
     title: handleKbQuery
     sourceFile: packages/mcp/src/tools/query.ts
@@ -49,7 +49,7 @@ symbols:
     sourceColumn: 22
     sourceEndLine: 91
     sourceEndColumn: 1
-    coordinatesGeneratedAt: '2026-03-28T18:53:57.275Z'
+    coordinatesGeneratedAt: '2026-03-31T09:19:46.729Z'
   - id: SYM-004
     title: handleKbCheck
     sourceFile: packages/mcp/src/tools/check.ts
@@ -65,7 +65,7 @@ symbols:
     sourceColumn: 22
     sourceEndLine: 219
     sourceEndColumn: 1
-    coordinatesGeneratedAt: '2026-03-28T18:53:57.353Z'
+    coordinatesGeneratedAt: '2026-03-31T09:19:46.811Z'
   - id: SYM-005
     title: KibiTreeDataProvider
     sourceFile: packages/vscode/src/treeProvider.ts
@@ -81,7 +81,7 @@ symbols:
     sourceColumn: 13
     sourceEndLine: 1002
     sourceEndColumn: 1
-    coordinatesGeneratedAt: '2026-03-28T18:53:57.481Z'
+    coordinatesGeneratedAt: '2026-03-31T09:19:46.978Z'
   - id: SYM-007
     title: extractFromManifest
     sourceFile: packages/cli/src/extractors/manifest.ts
@@ -94,7 +94,7 @@ symbols:
     sourceColumn: 16
     sourceEndLine: 176
     sourceEndColumn: 1
-    coordinatesGeneratedAt: '2026-03-28T18:53:57.536Z'
+    coordinatesGeneratedAt: '2026-03-31T09:19:47.049Z'
   - id: SYM-010
     title: startServer
     sourceFile: packages/mcp/src/server.ts
@@ -107,7 +107,7 @@ symbols:
     sourceColumn: 22
     sourceEndLine: 57
     sourceEndColumn: 1
-    coordinatesGeneratedAt: '2026-03-28T18:53:57.707Z'
+    coordinatesGeneratedAt: '2026-03-31T09:19:47.276Z'
   - id: SYM-KibiTreeDataProvider
     title: KibiTreeDataProvider
     sourceFile: packages/vscode/src/treeProvider.ts
@@ -123,7 +123,7 @@ symbols:
     sourceColumn: 13
     sourceEndLine: 1002
     sourceEndColumn: 1
-    coordinatesGeneratedAt: '2026-03-28T18:53:57.707Z'
+    coordinatesGeneratedAt: '2026-03-31T09:19:47.276Z'
   - id: SYM-KibiCodeActionProvider
     title: KibiCodeActionProvider
     sourceFile: packages/vscode/src/codeActionProvider.ts
@@ -138,7 +138,7 @@ symbols:
     sourceColumn: 13
     sourceEndLine: 106
     sourceEndColumn: 1
-    coordinatesGeneratedAt: '2026-03-28T18:53:57.708Z'
+    coordinatesGeneratedAt: '2026-03-31T09:19:47.277Z'
   - id: SYM-handleKbQueryRelationships
     title: handleKbQueryRelationships
     sourceFile: packages/mcp/src/tools/query-relationships.ts
@@ -170,7 +170,7 @@ symbols:
     sourceColumn: 16
     sourceEndLine: 91
     sourceEndColumn: 1
-    coordinatesGeneratedAt: '2026-03-28T18:53:57.710Z'
+    coordinatesGeneratedAt: '2026-03-31T09:19:47.278Z'
   - id: SYM-KibiCodeLensProvider
     title: KibiCodeLensProvider
     sourceFile: packages/vscode/src/codeLensProvider.ts
@@ -185,7 +185,7 @@ symbols:
     sourceColumn: 13
     sourceEndLine: 334
     sourceEndColumn: 1
-    coordinatesGeneratedAt: '2026-03-28T18:53:57.821Z'
+    coordinatesGeneratedAt: '2026-03-31T09:19:47.387Z'
   - id: SYM-mergeStaticLinks
     title: mergeStaticLinks
     sourceFile: packages/vscode/src/codeLensProvider.ts
@@ -230,7 +230,7 @@ symbols:
     sourceColumn: 16
     sourceEndLine: 102
     sourceEndColumn: 1
-    coordinatesGeneratedAt: '2026-03-30T09:23:50.000Z'
+    coordinatesGeneratedAt: '2026-03-31T09:19:47.464Z'
   - id: SYM-checkWorkspaceHealth
     title: checkWorkspaceHealth
     sourceFile: packages/opencode/src/workspace-health.ts
@@ -241,8 +241,8 @@ symbols:
         target: REQ-opencode-kibi-plugin-v1
       - type: covered_by
         target: TEST-opencode-kibi-plugin-v1
-    sourceLine: 30
+    sourceLine: 31
     sourceColumn: 16
-    sourceEndLine: 86
+    sourceEndLine: 87
     sourceEndColumn: 1
-    coordinatesGeneratedAt: '2026-03-29T20:24:42.644Z'
+    coordinatesGeneratedAt: '2026-03-31T09:19:47.531Z'

documentation/tests/TEST-mcp-upsert-coverage.md

@@ -0,0 +1,23 @@
+---
+id: TEST-mcp-upsert-coverage
+title: MCP upsert handler unit coverage exercises validation and failure paths
+status: active
+created_at: 2026-03-30T00:00:00Z
+updated_at: 2026-03-30T00:00:00Z
+priority: must
+tags:
+  - mcp
+  - test
+  - upsert
+  - coverage
+source: packages/mcp/tests/tools/upsert.test.ts
+links:
+  - REQ-002
+  - REQ-011
+---
+
+Validation steps:
+- run `bun test packages/mcp/tests/tools/upsert.test.ts packages/mcp/tests/tools/upsert-contradictions.test.ts packages/mcp/tests/tools/crud.test.ts`
+- run `bun test --coverage packages/mcp/tests/tools/upsert.test.ts packages/mcp/tests/tools/upsert-contradictions.test.ts packages/mcp/tests/tools/crud.test.ts`
+- verify `packages/mcp/src/tools/upsert.ts` reports 100% line coverage
+- verify mocked paths cover validation, contradiction formatting, audit/save failures, and symbol refresh warnings

packages/cli/CHANGELOG.md

@@ -1,5 +1,11 @@
 # kibi-cli
 
+## 0.4.2
+
+### Patch Changes
+
+- 7309d18: Export `__test__` helpers from `traceability/validate.ts` to enable unit testing of internal Prolog parsing utilities.
+
 ## 0.4.1
 
 ### Patch Changes

packages/cli/package.json

@@ -1,6 +1,6 @@
 {
   "name": "kibi-cli",
-  "version": "0.4.1",
+  "version": "0.4.2",
   "type": "module",
   "description": "Kibi CLI for knowledge base management",
   "engines": {

packages/cli/src/extractors/symbols-coordinator.ts

@@ -40,6 +40,7 @@ export async function enrichSymbolCoordinates(
   entries: ManifestSymbolEntry[],
   workspaceRoot: string,
 ): Promise<ManifestSymbolEntry[]> {
+  // implements REQ-vscode-traceability
   const output = entries.map((entry) => ({ ...entry }));
 
   const tsIndices: number[] = [];

packages/cli/src/extractors/symbols-ts.ts

@@ -62,13 +62,13 @@ export async function enrichSymbolCoordinatesWithTsMorph(
   entries: ManifestSymbolEntry[],
   workspaceRoot: string,
 ): Promise<ManifestSymbolEntry[]> {
+  // implements REQ-vscode-traceability
   const project = new Project({
     skipAddingFilesFromTsConfig: true,
   });
   const sourceFileCache = new Map<string, SourceFile>();
 
   const enriched: ManifestSymbolEntry[] = [];
-
   for (const entry of entries) {
     try {
       const resolved = resolveSourcePath(entry.sourceFile, workspaceRoot);

packages/cli/src/traceability/validate.ts

@@ -185,3 +185,11 @@ export function formatViolations(violations: Violation[]): string {
   }
   return lines.join("\n");
 }
+
+// Test helpers for edge-case coverage
+export const __test__ = {
+  unquoteAtom,
+  splitTopLevelComma,
+  splitTopLevelLists,
+  parsePrologListOfLists,
+};