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

Author: data-douser

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

@@ -0,0 +1,17 @@
+# `codeql_lsp_completion/basic_completion`
+
+## PURPOSE
+
+Tests that `codeql_lsp_completion` returns completion items when the cursor is
+positioned on a type name in a `from` clause of a CodeQL query.
+
+## INPUTS
+
+- **file_path**: `server/ql/javascript/examples/src/ExampleQuery1/ExampleQuery1.ql`
+- **line**: 12 (on the type name in the `from` clause)
+- **character**: 7 (cursor on the type name)
+
+## EXPECTED OUTPUTS
+
+- A list of completion items (may be empty if no workspace URI is set).
+- Monitoring state updated to record a successful `codeql_lsp_completion` call.

client/integration-tests/primitives/tools/codeql_lsp_definition/basic_definition/README.md

@@ -0,0 +1,17 @@
+# `codeql_lsp_definition/basic_definition`
+
+## PURPOSE
+
+Tests that `codeql_lsp_definition` returns definition locations when the cursor
+is on a variable name in a `where` clause of a CodeQL query.
+
+## INPUTS
+
+- **file_path**: `server/ql/javascript/examples/src/ExampleQuery1/ExampleQuery1.ql`
+- **line**: 13 (on a variable reference in the `where` clause)
+- **character**: 6 (cursor on the variable name)
+
+## EXPECTED OUTPUTS
+
+- One or more definition locations, or an empty list if the symbol is not resolvable.
+- Monitoring state updated to record a successful `codeql_lsp_definition` call.

client/integration-tests/primitives/tools/codeql_lsp_diagnostics/semantic_validation/README.md

@@ -0,0 +1,17 @@
+# `codeql_lsp_diagnostics/semantic_validation`
+
+## PURPOSE
+
+Tests that `codeql_lsp_diagnostics` detects semantic errors in QL code that
+references undefined types (e.g., `UndefinedType`).
+
+## INPUTS
+
+- **ql_code**: A QL query fragment referencing `UndefinedType` which does not
+  exist, triggering a semantic "could not resolve type" diagnostic.
+
+## EXPECTED OUTPUTS
+
+- `isValid` is `false` with semantic diagnostics about unresolvable types.
+- The `semantic_query.ql` file remains unchanged (identical in before/ and after/).
+- Monitoring state updated to record a successful `codeql_lsp_diagnostics` call.

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

@@ -1,3 +1,6 @@
 {
-  "sessions": []
+  "sessions": [],
+  "parameters": {
+    "ql_code": "from UndefinedType x\nwhere x = \"test\"\nselect x, \"semantic error: undefined type\""
+  }
 }

client/integration-tests/primitives/tools/codeql_lsp_diagnostics/syntax_validation/README.md

@@ -0,0 +1,15 @@
+# `codeql_lsp_diagnostics/syntax_validation`
+
+## PURPOSE
+
+Tests that `codeql_lsp_diagnostics` detects syntax errors in invalid QL code.
+
+## INPUTS
+
+- **ql_code**: Invalid QL snippet with syntax errors (`invalid_type x\nwhere x = "test"\nselect x, "This has syntax errors"`).
+
+## EXPECTED OUTPUTS
+
+- `isValid` is `false` with one or more error diagnostics.
+- The `test_query.ql` file remains unchanged (identical in before/ and after/).
+- Monitoring state updated to record a successful `codeql_lsp_diagnostics` call.

client/integration-tests/primitives/tools/codeql_lsp_references/basic_references/README.md

@@ -0,0 +1,17 @@
+# `codeql_lsp_references/basic_references`
+
+## PURPOSE
+
+Tests that `codeql_lsp_references` returns reference locations when the cursor
+is on a variable name used in a `where` clause of a CodeQL query.
+
+## INPUTS
+
+- **file_path**: `server/ql/javascript/examples/src/ExampleQuery1/ExampleQuery1.ql`
+- **line**: 13 (on a variable reference in the `where` clause)
+- **character**: 6 (cursor on the variable name)
+
+## EXPECTED OUTPUTS
+
+- One or more reference locations, including the declaration.
+- Monitoring state updated to record a successful `codeql_lsp_references` call.

client/src/lib/integration-test-runner.js

@@ -737,10 +737,14 @@ export class IntegrationTestRunner {
       // Call the tool with appropriate parameters
       // Set extended timeout for long-running operations
       const longRunningTools = [
-        "codeql_query_run",
-        "codeql_test_run",
         "codeql_database_analyze",
-        "codeql_database_create"
+        "codeql_database_create",
+        "codeql_lsp_completion",
+        "codeql_lsp_definition",
+        "codeql_lsp_diagnostics",
+        "codeql_lsp_references",
+        "codeql_query_run",
+        "codeql_test_run"
       ];
 
       const requestOptions = longRunningTools.includes(toolName)

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

@@ -81,7 +81,7 @@
     "build": "npm run clean && npm run lint && npm run bundle",
     "build:all": "npm run build && npm run test:ql:fail-fast",
     "bundle": "node esbuild.config.js",
-    "clean": "rm -rf dist",
+    "clean": "rm -rf dist .tmp",
     "dev:stdio": "npm run build && TRANSPORT_MODE=stdio node dist/codeql-development-mcp-server.js",
     "dev:http": "npm run build && TRANSPORT_MODE=http node dist/codeql-development-mcp-server.js",
     "format": "prettier --write 'src/**/*.ts'",