Add search_ql_code and codeql_resolve_files tools

Add search_ql_code and codeql_resolve_files tools in order to
eliminate grep/CLI dependencies.

- New tools: search_ql_code (QL text/regex search) and codeql_resolve_files
  (file discovery by extension/glob) so LLMs never need shell access
- Rewrite profile_codeql_query_from_logs with two-tier design: compact
  inline JSON + line-indexed detail file for targeted read_file access;
  parser now captures RA operations and pipeline-stage tuple progressions
- Fix codeql_resolve_database to probe child directories for databases
- Remove all grep/CLI references from prompts and resources
- Cross-platform: normalize \r\n line endings in parser and search tool

Author: data-douser

client/integration-tests/primitives/tools/codeql_resolve_files/find_qll_files/README.md

@@ -0,0 +1,26 @@
+# Integration Test: codeql_resolve_files/find_qll_files
+
+## Purpose
+
+Tests the `codeql_resolve_files` tool to ensure it can find QL library files by extension within a CodeQL pack directory.
+
+## Test Scenario
+
+This test validates that the `codeql_resolve_files` tool can:
+
+1. Accept a directory path and file extension filter
+2. Use the `codeql resolve files` CLI command to find matching files
+3. Return a list of file paths matching the specified criteria
+
+## Test Parameters
+
+- `dir`: "server/ql/javascript/examples/src"
+- `include-extension`: [".ql"]
+
+## Expected Behavior
+
+The tool should:
+
+1. Invoke `codeql resolve files` with the specified directory and extension filter
+2. Return file paths for all `.ql` files found in the directory tree
+3. Return a successful result with the file listing

client/integration-tests/primitives/tools/codeql_resolve_files/find_qll_files/after/monitoring-state.json

@@ -0,0 +1,9 @@
+{
+  "toolName": "codeql_resolve_files",
+  "parameters": {
+    "dir": "server/ql/javascript/examples/src",
+    "include-extension": [".ql"]
+  },
+  "success": true,
+  "description": "Successfully resolved .ql files in JavaScript examples directory"
+}

client/integration-tests/primitives/tools/codeql_resolve_files/find_qll_files/before/monitoring-state.json

@@ -0,0 +1,9 @@
+{
+  "toolName": "codeql_resolve_files",
+  "parameters": {
+    "dir": "server/ql/javascript/examples/src",
+    "include-extension": [".ql"]
+  },
+  "expectedSuccess": true,
+  "description": "Test codeql_resolve_files for finding .ql files in JavaScript examples"
+}

client/integration-tests/primitives/tools/search_ql_code/search_predicate_name/README.md

@@ -0,0 +1,28 @@
+# Integration Test: search_ql_code/search_predicate_name
+
+## Purpose
+
+Tests the `search_ql_code` tool to ensure it can search QL source files for a predicate name pattern and return structured results with file paths and line numbers.
+
+## Test Scenario
+
+This test validates that the `search_ql_code` tool can:
+
+1. Accept a regex pattern for a predicate name
+2. Search `.ql` and `.qll` files in a given directory
+3. Return structured JSON results with file paths, line numbers, and matching lines
+4. Report the correct number of files searched and matches found
+
+## Test Parameters
+
+- `pattern`: "isSource"
+- `paths`: ["server/ql/javascript/examples/src"]
+- `contextLines`: 1
+
+## Expected Behavior
+
+The tool should:
+
+1. Recursively search `.ql` and `.qll` files in the specified directory
+2. Return matches with file paths, line numbers, and context lines
+3. Report `filesSearched`, `totalMatches`, `returnedMatches`, and `truncated` fields

client/integration-tests/primitives/tools/search_ql_code/search_predicate_name/after/monitoring-state.json

@@ -0,0 +1,23 @@
+{
+  "toolName": "search_ql_code",
+  "parameters": {
+    "pattern": "isSource",
+    "paths": ["server/ql/javascript/examples/src"],
+    "contextLines": 1
+  },
+  "success": true,
+  "description": "Successfully searched QL files for predicate name pattern",
+  "searchResult": {
+    "totalMatches": 1,
+    "returnedMatches": 1,
+    "truncated": false,
+    "filesSearched": 1,
+    "results": [
+      {
+        "filePath": "server/ql/javascript/examples/src/ExampleQuery1/ExampleQuery1.ql",
+        "lineNumber": 1,
+        "lineContent": "contains isSource match"
+      }
+    ]
+  }
+}

client/integration-tests/primitives/tools/search_ql_code/search_predicate_name/before/monitoring-state.json

@@ -0,0 +1,10 @@
+{
+  "toolName": "search_ql_code",
+  "parameters": {
+    "pattern": "isSource",
+    "paths": ["server/ql/javascript/examples/src"],
+    "contextLines": 1
+  },
+  "expectedSuccess": true,
+  "description": "Test search_ql_code for predicate name search in JavaScript examples"
+}

extensions/vscode/test/suite/mcp-tool-e2e.integration.test.ts

@@ -144,6 +144,8 @@ suite('MCP Server Tool Integration Tests', () => {
     assert.ok(toolNames.includes('list_codeql_databases'), 'Should include list_codeql_databases');
     assert.ok(toolNames.includes('list_query_run_results'), 'Should include list_query_run_results');
     assert.ok(toolNames.includes('list_mrva_run_results'), 'Should include list_mrva_run_results');
+    assert.ok(toolNames.includes('search_ql_code'), 'Should include search_ql_code');
+    assert.ok(toolNames.includes('codeql_resolve_files'), 'Should include codeql_resolve_files');
 
     console.log(`[mcp-tool-e2e] Server provides ${response.tools.length} tools`);
   });