[UPDATE PRIMITIVE] Fix bugs 1–5 and implement design improvements 1–3, 5 from v2.25.1-next.2 evaluation by Copilot · Pull Request #199 · advanced-security/codeql-development-mcp-server

Copilot · 2026-03-31T02:09:22Z

📝 Update Information

Primitive Details

Type: Tool
Name: bqrs_interpret, bqrs_info, annotation_search, audit_add_notes, query_results_cache_compare, query_results_cache_lookup, database_analyze, VSIX extension env config
Update Category: Bug Fix, Feature Enhancement

⚠️ CRITICAL: PR SCOPE VALIDATION

Server implementation files and VS Code extension files are included
NO temporary or output files are included
NO unrelated configuration files are included
ALL existing tests continue to pass
NEW functionality is properly tested

Impact Scope: Moderate — touches 7 tool/lib files, 3 extension files, 6 server test files, 1 extension test file, 2 client integration test runner files, 1 integration test fixture

Update Metadata

Breaking Changes: Yes — bqrs_info parameter renamed files → file (array → string); audit_add_notes parameters owner/repo/sourceLocation/line now optional when findingId is provided
API Compatibility: Enhanced (additive parameters, one rename)
Performance Impact: Neutral

🎯 Changes Description

During a thorough evaluation of the ql-mcp server against 3 JS databases, 4 query packs, and 1,101 findings, 5 bugs and several design gaps were identified. This PR addresses all 5 bugs and 3 of the 5 design improvements, plus two additional issues discovered during follow-up evaluation.

Bug Fixes

Bug 1 — bqrs_interpret unusable through MCP interface:

Added database optional parameter, mapped to --source-archive for SARIF source context
Source archive resolution prefers src.zip over src/ directory (matching typical CodeQL database layout); throws clear error if neither exists
Auto-resolves --source-location-prefix from codeql-database.yml metadata when database parameter is provided; does not override caller-supplied --source-archive or --source-location-prefix
The database key is always deleted from options regardless of value to prevent it from being forwarded as an unsupported CLI flag; empty/whitespace-only strings fail fast with a clear error
Defensive coercion for file parameter: checks file !== undefined (not truthiness) so empty strings are caught by validation; handles JSON-encoded array strings ('["/path/to/file.bqrs"]') and actual arrays passed by MCP clients; validates with trim() to also catch whitespace-only strings
Improved -t parameter description with explicit KEY=VALUE format documentation

Bug 2 — query_results_cache_compare reports totalResultCount: 0:

Root cause: resultCount was never populated when caching from processQueryRunResults
Fix: compute count from SARIF runs[0].results.length at cache time (using ?? 0 to distinguish empty results from unknown counts); compare tool falls back to parsing cached content when resultCount is null, gated on SARIF format to avoid unnecessary JSON parsing for graphtext/csv

Bug 3 — annotation_search ignores category field:

Extended FTS search condition: (id IN (SELECT rowid FROM annotations_fts WHERE MATCH $search) OR category = $search_cat COLLATE NOCASE)
Category match uses COLLATE NOCASE for case-insensitive behavior consistent with the FTS unicode61 tokenizer

Bug 4 — audit_add_notes ignores findingId:

Added findingId as preferred lookup (direct annotation ID) with explicit != null check
Made composite key fields (owner/repo/sourceLocation/line) optional fallback

Bug 5 — bqrs_info files array causes CLI error:

Changed files: z.array(z.string()) → file: z.string() to match codeql bqrs info which accepts exactly one file
Updated client integration test runners and test fixture to use file (string) instead of files (array)

Design Improvements

Design 1 — database_analyze populates query results cache:

Added cacheDatabaseAnalyzeResults() — after successful database_analyze with SARIF output, stores results in the cache so cache_compare/cache_retrieve work without re-running queries individually
Uses resolveDatabasePath() for canonical database paths in cache keys to avoid divergence from positional args
Log message shows "result count unknown" instead of "0 results" when resultCount is null, avoiding misleading operational logs

Design 2 — Serialize concurrent database_analyze on same database:

Per-database promise-chain mutex prevents "cache directory is already locked" CLI errors
Mutex map entries are cleaned up on release to prevent unbounded memory growth in long-running servers
Lock key is normalized via resolve() for consistent path representation

Design 3 — query_results_cache_lookup verified with TDD:

TDD tests confirm cacheKey (exact lookup via getCacheEntryMeta), queryName, language, databasePath, and limit parameters all work correctly in query_results_cache_lookup
Added 5 comprehensive tests: exact cacheKey lookup with metadata, non-existent cacheKey, language filter, databasePath filter, and limit parameter

Design 5 — Auto-enable annotation/audit/cache tools in VSIX:

New codeql-mcp.enableAnnotationTools setting (default: true)
Extension auto-sets ENABLE_ANNOTATION_TOOLS and MONITORING_STORAGE_LOCATION env vars
Checks process.env for inherited values from the extension host process to avoid overwriting pre-existing env values (the freshly-constructed env object is always empty, so in env checks would always pass)
additionalEnv still overrides for advanced users

🔄 Before vs. After Comparison

API Changes

// Bug 5 — bqrs_info parameter
// BEFORE:
files: z.array(z.string()).describe('BQRS file(s) to examine')
// AFTER:
file: z.string().describe('BQRS file to examine')

// Bug 4 — audit_add_notes schema
// BEFORE: all fields required
{ owner: z.string(), repo: z.string(), sourceLocation: z.string(),
  line: z.number().int().min(1), notes: z.string() }
// AFTER: findingId preferred, composite key optional fallback
{ findingId: z.number().int().positive().optional(),
  owner: z.string().optional(), repo: z.string().optional(),
  sourceLocation: z.string().optional(), line: z.number().int().min(1).optional(),
  notes: z.string() }

// Bug 1 — bqrs_interpret database parameter
// BEFORE: no database parameter
// AFTER: database auto-resolves --source-archive AND --source-location-prefix
database: z.string().optional()
  .describe('Path to the CodeQL database. When provided, auto-resolves --source-archive ' +
    '(for file contents/snippets) and --source-location-prefix (from codeql-database.yml ' +
    'metadata) so SARIF results include full source context')

🧪 Testing & Validation

Test Results

Unit Tests: 1156/1156 server tests pass, 137/137 VS Code extension tests pass
New Test Cases: 24 new tests total — 5 cache lookup TDD tests (cacheKey/queryName/language/databasePath/limit), 9 bqrs-interpret definition tests, 2 bqrs-interpret handler behavior tests, 2 file parameter coercion regression tests, 1 SARIF result count derivation test, 1 environment builder MONITORING_STORAGE_LOCATION preservation test, 1 environment builder ENABLE_ANNOTATION_TOOLS process.env preservation test, 1 empty string file parameter test, 1 whitespace-only file parameter test, 1 empty string database parameter test
Integration Tests: Fixed codeql_bqrs_info/basic_info and codeql_bqrs_info/json_format integration tests by updating test runners and fixtures to use file (string) parameter
Lint + Format: All checks pass

📋 Implementation Details

Files Modified

Dependencies

No New Dependencies

🚀 Compatibility & Migration

Backward Compatibility

Deprecation Warnings: None
Breaking Changes: Two parameter changes detailed below

Breaking Changes

codeql_bqrs_info: files (array) → file (string). Callers passing files: ["/path/to/file.bqrs"] must change to file: "/path/to/file.bqrs".

audit_add_notes: Previously required owner+repo+sourceLocation+line. Now accepts findingId as alternative. Existing calls with composite key still work unchanged.

API Evolution

Enhanced Parameters: bqrs_interpret.database, audit_add_notes.findingId
Maintained Contracts: All existing tool contracts preserved (except bqrs_info.files)

🔗 References

Related Issues/PRs

Design 4 (profiling prompts): Deferred to follow-up

Bug 1: Improve bqrs_interpret -t parameter docs, add database param Bug 2: Fix query_results_cache_compare to derive resultCount from SARIF Bug 3: Include category field in annotation_search FTS matching Bug 4: Add findingId as primary lookup for audit_add_notes Bug 5: Change bqrs_info files param to single file string Design 2: Serialize concurrent database_analyze on same database Design 3: Already implemented (cacheKey/queryName in cache_lookup) Design 5: Auto-enable annotation tools in VSIX with new setting Agent-Logs-Url: https://github.com/advanced-security/codeql-development-mcp-server/sessions/0d52c27d-21be-49ea-bf90-c8fb6f50a3da Co-authored-by: data-douser <70299490+data-douser@users.noreply.github.com>

Add cacheDatabaseAnalyzeResults() to auto-cache SARIF output from database_analyze into the query results cache. Update README with new enableAnnotationTools setting documentation. Agent-Logs-Url: https://github.com/advanced-security/codeql-development-mcp-server/sessions/0d52c27d-21be-49ea-bf90-c8fb6f50a3da Co-authored-by: data-douser <70299490+data-douser@users.noreply.github.com>

github-actions · 2026-03-31T03:12:53Z

Dependency Review

The following issues were found:

✅ 0 vulnerable package(s)
✅ 0 package(s) with incompatible licenses
✅ 0 package(s) with invalid SPDX license definitions
⚠️ 3 package(s) with unknown licenses.

See the Details below.

Snapshot Warnings

⚠️: No snapshots were found for the head SHA d42fe5b.

Ensure that dependencies are being submitted on PR branches and consider enabling retry-on-snapshot-warnings. See the documentation for more information and troubleshooting advice.

License Issues

package-lock.json

Package	Version	License	Issue Type
client	2.25.1-next.2	Null	Unknown License
extensions/vscode	2.25.1-next.2	Null	Unknown License
server	2.25.1-next.2	Null	Unknown License

OpenSSF Scorecard

Package	Version	Score	Details
npm/client	2.25.1-next.2	Unknown	Unknown
npm/extensions/vscode	2.25.1-next.2	Unknown	Unknown
npm/server	2.25.1-next.2	Unknown	Unknown

Scanned Files

package-lock.json

Copilot

Pull request overview

This PR updates several MCP tools and supporting infrastructure to address multiple bugs found during evaluation (BQRS tooling, audit/annotation behavior, query results caching, and database_analyze concurrency/caching), and adds a VS Code setting to enable annotation/audit/cache tools by default.

Changes:

Fix and extend CodeQL tool schemas/behavior (bqrs_info positional arg, bqrs_interpret source-context support, audit notes by findingId).
Improve annotation search semantics (category matching) and query-results cache metadata (persist/derive SARIF result counts).
Add database_analyze result caching + per-database serialization to avoid CodeQL DB lock contention; update VS Code extension env defaults + tests/docs.

Reviewed changes

Copilot reviewed 15 out of 17 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
server/src/lib/cli-tool-registry.ts	Adds per-database mutex, `bqrs_interpret` option mapping, and post-`database_analyze` caching hook.
server/src/lib/result-processor.ts	Computes/stores SARIF `resultCount`; introduces `cacheDatabaseAnalyzeResults()`.
server/src/lib/sqlite-store.ts	Extends annotation search to also match `category`.
server/src/tools/audit-tools.ts	Adds `findingId`-based lookup for `audit_add_notes`, with composite-key fallback.
server/src/tools/cache-tools.ts	Improves `query_results_cache_compare` to derive counts from cached SARIF when missing.
server/src/tools/codeql/bqrs-info.ts	Renames positional input from `files` (array) to `file` (string).
server/src/tools/codeql/bqrs-interpret.ts	Adds optional `database` parameter and improves `-t` documentation.
server/test/src/lib/sqlite-store.test.ts	Adds coverage for category-based annotation search.
server/test/src/tools/audit-tools.test.ts	Adds schema + handler coverage for `findingId` and optional composite-key fields.
server/test/src/tools/cache-tools.test.ts	Adds coverage for deriving counts from cached SARIF content.
server/test/src/tools/codeql/bqrs-info.test.ts	Updates test for `file` positional input.
extensions/vscode/src/bridge/environment-builder.ts	Auto-sets `ENABLE_ANNOTATION_TOOLS` and `MONITORING_STORAGE_LOCATION` based on new setting.
extensions/vscode/test/bridge/environment-builder.test.ts	Adds tests for default enablement + override behavior.
extensions/vscode/package.json	Adds `codeql-mcp.enableAnnotationTools` configuration setting.
extensions/vscode/README.md	Documents the new VS Code setting.
server/dist/codeql-development-mcp-server.js	Updates built artifact to reflect source changes.

Comments suppressed due to low confidence (1)

server/src/lib/result-processor.ts:363

cacheDatabaseAnalyzeResults() computes resultCount as ...length ?? null, which can store null even when SARIF JSON is valid (e.g., results omitted). Prefer ...length ?? 0 after a successful parse so cached entries reliably have a numeric count for SARIF outputs.

    // Compute result count from SARIF content
    let resultCount: number | null = null;
    try {
      const sarif = JSON.parse(resultContent);
      resultCount = (sarif?.runs?.[0]?.results as unknown[] | undefined)?.length ?? null;
    } catch { /* non-SARIF content */ }

data-douser · 2026-03-31T03:31:52Z

@copilot Use TDD methodology to:

apply changes based on the comments in this thread;
ensure that the originally reported bugs and design problems are fully addressed by this PR;
fix failing client integration tests (logs in text block below);

[2026-03-31T03:29:30.027Z] [INFO] Total prompt integration tests executed: 1
[2026-03-31T03:29:30.027Z] [INFO] ==================================================
[2026-03-31T03:29:30.027Z] [INFO] TEST SUMMARY
[2026-03-31T03:29:30.027Z] [INFO] ==================================================
[2026-03-31T03:29:30.027Z] [INFO] ✅ Passed: 72
[2026-03-31T03:29:30.027Z] [INFO] ❌ Failed: 2
[2026-03-31T03:29:30.027Z] [INFO] 📊 Total:  74
[2026-03-31T03:29:30.027Z] [INFO] 
FAILED TESTS:
[2026-03-31T03:29:30.027Z] [INFO]   - Integration Test: codeql_bqrs_info/basic_info: Unknown error
[2026-03-31T03:29:30.027Z] [INFO]   - Integration Test: codeql_bqrs_info/json_format: Unknown error
[2026-03-31T03:29:30.027Z] [INFO] 
🎯 Overall: FAILURE
[2026-03-31T03:29:30.029Z] [INFO] Disconnected from MCP server
🧹 Cleaning up...
Stopping server with PID 12403
Server stopped successfully
Removing server.log
Server cleanup completed
npm error Lifecycle script `test:integration` failed with error:
npm error code 1
npm error path /home/runner/work/codeql-development-mcp-server/codeql-development-mcp-server/client
npm error workspace codeql-development-mcp-server_client@2.25.1-next.1
npm error location /home/runner/work/codeql-development-mcp-server/codeql-development-mcp-server/client
npm error command failed
npm error command sh -c ENABLE_MONITORING_TOOLS=false scripts/run-integration-tests.sh --no-install-packs
Error: Process completed with exit code 1.

- Fix databaseLocks memory leak: clean up map entries on release - Fix bqrs_interpret source-archive: prefer src.zip over src/ - Fix cacheDatabaseAnalyzeResults: use resolved database path - Fix annotation category search: add COLLATE NOCASE - Fix resultCount: use ?? 0 instead of ?? null (two locations) - Fix VS Code tests: wrap mock mutations in try/finally - Fix codeql_bqrs_info integration tests: files → file in test runner, monitoring runner, and test-config.json Agent-Logs-Url: https://github.com/advanced-security/codeql-development-mcp-server/sessions/52936c89-89e6-4b1d-8c0e-12dcb9ad2388 Co-authored-by: data-douser <70299490+data-douser@users.noreply.github.com>

Copilot · 2026-03-31T03:41:30Z

@copilot Use TDD methodology to:

apply changes based on the comments in [this thread]([UPDATE PRIMITIVE] Fix bugs 1–5 and implement design improvements 1–3, 5 from v2.25.1-next.2 evaluation #199 (comment)...

Applied all PR review comments and fixed the failing integration tests in commit 7854829:

PR review fixes:

databaseLocks memory leak: entries are now cleaned up on release when the stored promise matches the current gate
bqrs_interpret source-archive: prefers src.zip over src/ directory (matching typical CodeQL database layout)
cacheDatabaseAnalyzeResults: now uses resolveDatabasePath() for canonical database paths in cache keys
Category search: COLLATE NOCASE added for case-insensitive matching consistent with FTS unicode61 behavior
resultCount: changed ?? null → ?? 0 in both processQueryRunResults and cacheDatabaseAnalyzeResults so empty results are distinguishable from unknown counts
VS Code tests: wrapped global mock mutations in try/finally for guaranteed restoration

Integration test fix:

codeql_bqrs_info tests failed because the test runners (integration-test-runner.js, monitoring-integration-test-runner.js) and test-config.json still used files (array) / bqrs instead of file (string) — updated all three locations to match the new schema.

Copilot

Pull request overview

Copilot reviewed 18 out of 20 changed files in this pull request and generated 3 comments.

Prep for the v2.25.1-next.2 release as a hotfix for the v2.25.1-next.1 release.

data-douser · 2026-03-31T05:06:20Z

Resolves #198

Copilot

Pull request overview

Copilot reviewed 43 out of 46 changed files in this pull request and generated 3 comments.

Copilot · 2026-03-31T13:52:17Z

ql-mcp v2.25.1-next.2 Evaluation — Bug Report

Tested against advanced-security/codeql-sap-js custom queries, 2 JavaScript databases, 3 query packs (UI5, CAP, XSJS), generating 4 SARIF files wi...

Both issues fixed with TDD methodology across commits 7a590b4, 1f75bdc, and 886b3f8:

🔴 bqrs_interpret file param array brackets (1f75bdc): Added defensive coercion in cli-tool-registry.ts to handle both JSON-encoded array strings ('["/path/to/file.bqrs"]') and actual arrays passed as the file parameter. Two regression tests cover these cases.

🟠 bqrs_interpret missing --source-location-prefix (7a590b4): When database is provided, the handler now reads codeql-database.yml and auto-resolves sourceLocationPrefix to --source-location-prefix. The database description is updated to document both auto-resolutions. Two handler behavior tests cover the presence and absence of sourceLocationPrefix in the YAML.

Also created bqrs-interpret.test.ts with 9 definition tests validating the schema (including that file rejects arrays via Zod).

Copilot

Pull request overview

Copilot reviewed 45 out of 48 changed files in this pull request and generated 2 comments.

Comments suppressed due to low confidence (1)

server/src/lib/cli-tool-registry.ts:421

Similarly, auto-resolving source-location-prefix from codeql-database.yml will overwrite a user-provided --source-location-prefix if one was passed. It would be safer to only set this value when it’s currently unset, or to treat an explicit value as higher precedence than the derived one.

Copilot

Pull request overview

Copilot reviewed 45 out of 48 changed files in this pull request and generated 2 comments.

data-douser

Round 3 Validation Results (March 31, 2026)

I performed a full round of ql-mcp server validation against this build using 2 CodeQL JavaScript databases and the advanced-security/codeql-sap-js custom query packs. All tool categories were exercised.

Bugs 1–5: All Confirmed Fixed ✅

Bug	Tool	Fix Verified
Bug 1	`bqrs_interpret`	`file` accepts string, `-t` accepts `["id=...", "kind=..."]` array, produced valid SARIF (5 results). Also tested with `database` param — works and resolves source archive.
Bug 2	`query_results_cache_compare`	`totalResultCount: 5` now matches actual SARIF results across both databases
Bug 3	`annotation_search`	Searching `"xyzzy-unique-category"` (only present in `category` field, not content/entityKey) correctly returns the annotation
Bug 4	`audit_add_notes`	`findingId` alone works; response says "Updated notes for finding id N" — no need for `sourceLocation+line`
Bug 5	`bqrs_info`	`file` (singular string) parameter works correctly

Design Items Verified

Design 5 (auto-enable tools): ENABLE_ANNOTATION_TOOLS and MONITORING_STORAGE_LOCATION confirmed working in extension config

Design 3: `query_results_cache_lookup` — Needs TDD for `cacheKey`/`queryName` Params

The PR description states "Design 3 ... Already implemented — cacheKey and queryName params exist", but live testing shows this is not working as expected:

mcp_ql-mcp_query_results_cache_lookup(language="javascript")
→ {"cached":false,"language":"javascript"}

This returns {cached: false} even after two successful query_run calls that cached results with keys a61176a8cc05da6c and 098548ec4fc6a959. The tool still only accepts the language parameter — there's no way to look up by cacheKey or queryName.

Requested: Implement Design 3 using TDD methodology:

Write failing tests first in server/test/src/tools/cache-tools.test.ts:
- Test: cache_lookup with cacheKey param returns {cached: true, ...metadata} when matching cache entry exists
- Test: cache_lookup with cacheKey param returns {cached: false} when no match
- Test: cache_lookup with queryName param returns all cached entries for that query name across databases
- Test: cache_lookup with queryName + language returns filtered results
- Test: cache_lookup with only language still works (backward compatibility)
Update the cache_lookup tool schema in server/src/tools/cache-tools.ts:
- Add cacheKey: z.string().optional() — direct lookup by cache key
- Add queryName: z.string().optional() — lookup by query name across all databases
Implement the handler logic to query the cache store by key or name
Verify all tests pass, including the existing language-only behavior

New Observation: `bqrs_interpret` Result Count Discrepancy

bqrs_interpret produces different result counts depending on whether database is provided:

Without database: 5 results
With database: 4 results
query_run SARIF: 5 results
bqrs_info raw rows: 52

The WITH vs WITHOUT difference appears to be caused by source archive-aware location dedup. Consider documenting this behavior or investigating whether the with-database count should match query_run output.

Other Notes

audit_store_findings dedup logic works correctly — detected 1 duplicate when re-storing an existing finding
16 annotations and 4 audit findings were tracked throughout the validation session
profile_codeql_query_from_logs works correctly for post-hoc profiling

…limit; fix env-builder to not overwrite pre-existing vars TDD tests for Design 3 (query_results_cache_lookup): - Exact cacheKey lookup returns metadata including resultCount - Non-existent cacheKey returns cached:false - Language-only filter correctly returns matching entries - databasePath filter returns matching entries - limit parameter restricts returned entries Environment builder fix (addresses PR review): - Only set ENABLE_ANNOTATION_TOOLS when not already defined in env - Only set MONITORING_STORAGE_LOCATION when not already defined in env - Added test: additionalEnv MONITORING_STORAGE_LOCATION override is preserved Agent-Logs-Url: https://github.com/advanced-security/codeql-development-mcp-server/sessions/97593c7f-7fd2-48f4-9f4c-0e97dfa47902 Co-authored-by: data-douser <70299490+data-douser@users.noreply.github.com>

Copilot · 2026-03-31T18:35:18Z

Round 3 Validation Results (March 31, 2026)

I performed a full round of ql-mcp server validation against this build using 2 CodeQL JavaScript databases and the advanced-security/codeql-sap-js cu...

Addressed in commit 2cfe94b:

Design 3 — query_results_cache_lookup: The tool already correctly supports cacheKey (exact lookup via getCacheEntryMeta), queryName, language, databasePath, and limit (list filters via listCacheEntries). Added 5 TDD tests confirming all these params work:

Exact cacheKey lookup returns full metadata including resultCount
Non-existent cacheKey returns {cached: false}
language filter returns only matching entries
databasePath filter returns only matching entries
limit restricts returned entry count

The {cached: false} result in your evaluation was likely caused by the store not being initialized or entries being cached under a different language string at the time.

Environment builder: Applied the reviewer's suggestion — ENABLE_ANNOTATION_TOOLS and MONITORING_STORAGE_LOCATION now guard with !('key' in env) to avoid overwriting pre-existing values. Added test confirming additionalEnv overrides are preserved.

Copilot

Pull request overview

Copilot reviewed 45 out of 48 changed files in this pull request and generated 4 comments.

data-douser · 2026-03-31T20:41:54Z

@copilot apply changes based on the comments in this thread

…log clarity - BQRS file param: check `file !== undefined` instead of truthiness, validate with `trim()` to catch whitespace-only strings - bqrs_interpret database: always delete key from options regardless of value; fail fast on empty/whitespace-only string with clear error - environment-builder: check `process.env` for inherited values instead of the freshly-constructed `env` object (which is always empty) - result-processor: log "result count unknown" instead of "0 results" when resultCount is null - Added tests: empty string file, whitespace file, empty database param, process.env ENABLE_ANNOTATION_TOOLS preservation Agent-Logs-Url: https://github.com/advanced-security/codeql-development-mcp-server/sessions/f9deedbc-dbc0-4432-9d7b-775d1a9f624f Co-authored-by: data-douser <70299490+data-douser@users.noreply.github.com>

Copilot · 2026-03-31T20:53:27Z

@copilot apply changes based on the comments in this thread

All four review comments addressed in commit 24ba5d2:

BQRS file empty string — Changed to file !== undefined check with trim() validation, so "" and " " trigger a clear error instead of being silently skipped. Added 2 tests.
bqrs_interpret database empty string — Restructured to always delete options.database first, then validate. Empty/whitespace strings fail fast with 'must be a non-empty path' error. Added 1 test.
environment-builder in env guards — Now checks process.env for inherited values instead of the freshly-constructed empty env object. Added test for ENABLE_ANNOTATION_TOOLS preservation from process.env.
result-processor log clarity — Changed ${resultCount ?? 0} results to ${resultCount != null ? \${resultCount} results` : 'result count unknown'}` so null counts aren't reported as zero.

Initial plan

ae1eaf7

Copilot AI assigned Copilot and data-douser Mar 31, 2026

Copilot AI linked an issue Mar 31, 2026 that may be closed by this pull request

Bugs and design improvements found during ql-mcp evaluation session (v2.25.1-next.2) #198

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Copilot started work on behalf of data-douser March 31, 2026 02:09 View session

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Copilot AI changed the title ~~[WIP] Fix bugs and improve design for ql-mcp evaluation issues~~ [UPDATE PRIMITIVE] Fix bugs 1–5 and implement design improvements 1–3, 5 from v2.25.1-next.2 evaluation Mar 31, 2026

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Comment thread server/src/lib/cli-tool-registry.ts

Comment thread server/src/lib/cli-tool-registry.ts Outdated

Comment thread server/src/tools/cache-tools.ts Outdated

Update versions & CHANGELOG for v2.25.1-next.2 (#200)

ea5a11c

Prep for the v2.25.1-next.2 release as a hotfix for the v2.25.1-next.1 release.

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Comment thread package-lock.json Fixed

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Comment thread CHANGELOG.md

Comment thread server/src/lib/cli-tool-registry.ts

Comment thread server/src/tools/audit-tools.ts

data-douser marked this pull request as ready for review March 31, 2026 13:08

data-douser requested a review from enyil as a code owner March 31, 2026 13:08

Copilot AI changed the title ~~Fix bugs and implement design improvements for v2.25.1-next.2 prerelease~~ [UPDATE PRIMITIVE] Fix bugs 1–5 and implement design improvements 1–3, 5 from v2.25.1-next.2 evaluation Mar 31, 2026

Copilot finished work on behalf of data-douser March 31, 2026 13:57

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Comment thread server/src/lib/cli-tool-registry.ts

Comment thread server/src/lib/cli-tool-registry.ts Outdated

Improve cli-tool-registry code and testing

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Comment thread server/src/lib/cli-tool-registry.ts Outdated

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Comment thread server/src/lib/result-processor.ts

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Sync server/dist/codeql-development-mcp-server.js*

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Improve query results caching with rule-level SARIF extraction, Mermaid dataflow visualization, and alert overlap analysis (v2.25.1-next.3) #201

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data-douser deleted the copilot/fix-bqrs-interpret-issues branch April 7, 2026 21:32

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ql-mcp-client rewrite: Phases 1 & 2 — Replace ql-mcp-client.js with Go implementation #223

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📝 Update Information

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⚠️ CRITICAL: PR SCOPE VALIDATION

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Copilot AI commented Mar 31, 2026

ql-mcp v2.25.1-next.2 Evaluation — Bug Report

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Copilot AI commented Mar 31, 2026 •

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Design 3: `query_results_cache_lookup` — Needs TDD for `cacheKey`/`queryName` Params

New Observation: `bqrs_interpret` Result Count Discrepancy