Improve MCP server integrations with codeql execute *-server servers (#29)

* Add CodeQL background server manager and LSP tools

Implements CodeQLServerManager for config-aware lifecycle management
of CodeQL's three background servers (language-server, query-server2,
cli-server) with session-isolated cache directories and automatic
restart on configuration changes.

Adds four LSP-based MCP tools:
- codeql_lsp_diagnostics (renamed from codeql_language_server_eval)
- codeql_lsp_completion
- codeql_lsp_definition
- codeql_lsp_references

Resolves #17 (server manager with config hashing, session isolation,
graceful shutdown) and #1 (LSP completion/definition/references tools).

* Fix server lifecycle bugs and replace hard-coded startup delays

- Fix duplicate --tuple-counting flag when both debug and
  tupleCounting are set in buildQueryServerArgs
- Fix non-awaited force-kill timers in query-server and
  language-server shutdown methods (process could outlive caller)
- Remove redundant process.on SIGINT/SIGTERM handlers from
  lsp-diagnostics (already handled by shutdownServerManager)
- Replace hard-coded setTimeout delays (1.5-2s) in server
  start() methods with waitForProcessReady utility that resolves
  on first stderr/stdout output or rejects on spawn failure
- Add comprehensive tests for process-ready utility

* Fix CI failures and improve LSP tool reliability

- Add LSP tools to longRunningTools (300s timeout) in integration
  test runner to prevent CI timeouts during JVM startup
- Convert relative workspace_uri to file:// URIs in lsp-handlers
- Replace synchronous readFileSync with async readFile
- Add isRunning() guards to LSP feature methods
- Guard exit notification in shutdown to prevent "not running" error
- Fix semantic_validation test to use resolvable QL code
- Centralize logger mock in test/setup.ts (removes 16 per-file mocks)
- Add server-manager getLanguageServer/getQueryServer/getCLIServer tests
- Clarify --debug/--tuple-counting arg ordering in server-config
- Add missing README.md files to integration test directories

* Address PR review comments & fix integration tests

* Fixes for codeql_lsp_* tool integration tests

* Address PR review comments from review #3773277390

- Fix race condition in server-manager getOrRestart: serialize concurrent
  calls per server type using pendingStarts map with async/await pattern
- Fix lsp-handlers filePath docstring: document that relative paths are
  accepted and resolved against getUserWorkspaceDir()
- Fix semantic_validation/syntax_validation READMEs: clarify that before/
  after .ql files differ (not identical as previously stated)
- Fix semantic_validation/after/monitoring-state.json: update parameter
  shape to use ql_code matching the codeql_lsp_diagnostics tool contract
- Add concurrent access serialization test for server-manager

* Address code-quality PR review feedback

Author: data-douser

client/integration-tests/README.md

@@ -127,7 +127,7 @@ Monitoring-based integration tests enable testing of MCP tools that previously c
 ## Example: Tool with Both File-Based and Monitoring Tests
 
 ```text
-client/integration-tests/primitives/tools/codeql_language_server_eval/
+client/integration-tests/primitives/tools/codeql_lsp_diagnostics/
 └── semantic_validation/
     ├── before/
     │   ├── semantic_query.ql          # File-based test input

client/integration-tests/primitives/tools/codeql_language_server_eval/semantic_validation/after/monitoring-state.json

@@ -0,0 +1,22 @@
+# `codeql_lsp_completion/basic_completion`
+
+## PURPOSE
+
+Tests that `codeql_lsp_completion` returns targeted completion items for a
+member-access expression. The cursor is positioned after `f.getBa` so the
+language server should return completions matching the prefix (e.g.
+`getBaseName`). Uses `file_content` to provide inline query text, which
+avoids disk I/O and produces a small, focused result set.
+
+## INPUTS
+
+- **file_content**: Inline QL with cursor after `f.getBa`
+- **file_path**: `server/ql/javascript/examples/src/ExampleQuery1/ExampleQuery1.ql`
+- **line**: 3 (`where f.getBa`)
+- **character**: 13 (end of `getBa` prefix)
+- **workspace_uri**: `server/ql/javascript/examples`
+
+## EXPECTED OUTPUTS
+
+- A list of completion items matching the `getBa` prefix (e.g. `getBaseName`).
+- Monitoring state updated to record a successful `codeql_lsp_completion` call.

client/integration-tests/primitives/tools/codeql_language_server_eval/semantic_validation/before/monitoring-state.json

@@ -0,0 +1,14 @@
+{
+  "sessions": [
+    {
+      "id": "integration_test_session",
+      "calls": [
+        {
+          "tool": "codeql_lsp_completion",
+          "timestamp": "2026-02-08T00:00:00.000Z",
+          "status": "success"
+        }
+      ]
+    }
+  ]
+}

client/integration-tests/primitives/tools/codeql_lsp_completion/basic_completion/README.md

@@ -0,0 +1,10 @@
+{
+  "sessions": [],
+  "parameters": {
+    "file_content": "import javascript\n\nfrom File f\nwhere f.getBa\nselect f",
+    "file_path": "server/ql/javascript/examples/src/ExampleQuery1/ExampleQuery1.ql",
+    "line": 3,
+    "character": 13,
+    "workspace_uri": "server/ql/javascript/examples"
+  }
+}

client/integration-tests/primitives/tools/codeql_lsp_completion/basic_completion/after/monitoring-state.json

@@ -0,0 +1,21 @@
+# `codeql_lsp_completion/from_clause_completion`
+
+## PURPOSE
+
+Tests that `codeql_lsp_completion` returns keyword completions when the cursor
+is positioned after a partial keyword `wh` following a `from` clause. Uses
+`file_content` to provide inline query text, producing a small set of
+completions (e.g. `where`) rather than an exhaustive type list.
+
+## INPUTS
+
+- **file_content**: Inline QL with cursor after `wh` prefix
+- **file_path**: `server/ql/javascript/examples/src/ExampleQuery1/ExampleQuery1.ql`
+- **line**: 3 (after `wh`)
+- **character**: 2 (end of `wh` prefix)
+- **workspace_uri**: `server/ql/javascript/examples`
+
+## EXPECTED OUTPUTS
+
+- A list of completion items matching the `wh` prefix (e.g. `where`).
+- Monitoring state updated to record a successful `codeql_lsp_completion` call.

client/integration-tests/primitives/tools/codeql_lsp_completion/basic_completion/before/monitoring-state.json

@@ -0,0 +1,14 @@
+{
+  "sessions": [
+    {
+      "id": "integration_test_session",
+      "calls": [
+        {
+          "tool": "codeql_lsp_completion",
+          "timestamp": "2026-02-08T00:00:00.000Z",
+          "status": "success"
+        }
+      ]
+    }
+  ]
+}

client/integration-tests/primitives/tools/codeql_lsp_completion/from_clause_completion/README.md

@@ -0,0 +1,10 @@
+{
+  "sessions": [],
+  "parameters": {
+    "file_content": "import javascript\n\nfrom File f\nwh",
+    "file_path": "server/ql/javascript/examples/src/ExampleQuery1/ExampleQuery1.ql",
+    "line": 3,
+    "character": 2,
+    "workspace_uri": "server/ql/javascript/examples"
+  }
+}

client/integration-tests/primitives/tools/codeql_lsp_completion/from_clause_completion/after/monitoring-state.json

@@ -0,0 +1,21 @@
+# `codeql_lsp_definition/basic_definition`
+
+## PURPOSE
+
+Tests that `codeql_lsp_definition` resolves the definition of a type used in a
+`from` clause. The cursor is on `File` (line 2, character 7) which should
+resolve to the `File` class definition in the JavaScript CodeQL library.
+Uses `file_content` to provide inline query text.
+
+## INPUTS
+
+- **file_content**: Inline QL with `from File f` clause
+- **file_path**: `server/ql/javascript/examples/src/ExampleQuery1/ExampleQuery1.ql`
+- **line**: 2 (on the `File` type in `from File f`)
+- **character**: 7 (cursor on `File`)
+- **workspace_uri**: `server/ql/javascript/examples`
+
+## EXPECTED OUTPUTS
+
+- One or more definition locations with URIs pointing to `.qll` library files.
+- Monitoring state updated to record a successful `codeql_lsp_definition` call.