feat: query result caching and efficiency improvements

Always-on:
- Deduplicate resolveQueryPath (pass to processQueryRunResults)
- Cache resolveDatabasePath via module-level Map
- Cache extractQueryMetadata with mtime invalidation
- Track actual vs target CodeQL CLI version; warn on mismatch

Gated by ENABLE_ANNOTATION_TOOLS:
- query_result_cache table in SqliteStore with auto-populate
- query_results_cache_{lookup,retrieve,clear,compare} tools
- Subset retrieval: line range, grep, SARIF index/file filters

Integration tests:
- Add annotation mode to run-integration-tests.sh
- Client fixtures for all 4 cache tools
- Extension e2e: cache tool availability + workflow tests

Author: data-douser

client/integration-tests/primitives/tools/query_results_cache_clear/clear_all/after/monitoring-state.json

@@ -0,0 +1,8 @@
+{
+  "toolName": "query_results_cache_clear",
+  "parameters": {
+    "all": true
+  },
+  "success": true,
+  "description": "Successfully cleared all cached query results"
+}

client/integration-tests/primitives/tools/query_results_cache_clear/clear_all/before/monitoring-state.json

@@ -0,0 +1,8 @@
+{
+  "toolName": "query_results_cache_clear",
+  "parameters": {
+    "all": true
+  },
+  "expectedSuccess": true,
+  "description": "Test query_results_cache_clear clears all cached query results"
+}

client/integration-tests/primitives/tools/query_results_cache_clear/clear_all/test-config.json

@@ -0,0 +1,6 @@
+{
+  "toolName": "query_results_cache_clear",
+  "arguments": {
+    "all": true
+  }
+}

client/integration-tests/primitives/tools/query_results_cache_compare/compare_across_databases/after/monitoring-state.json

@@ -0,0 +1,8 @@
+{
+  "toolName": "query_results_cache_compare",
+  "parameters": {
+    "queryName": "CallGraphFrom"
+  },
+  "success": true,
+  "description": "Successfully compared cached query results across databases"
+}

client/integration-tests/primitives/tools/query_results_cache_compare/compare_across_databases/before/monitoring-state.json

@@ -0,0 +1,8 @@
+{
+  "toolName": "query_results_cache_compare",
+  "parameters": {
+    "queryName": "CallGraphFrom"
+  },
+  "expectedSuccess": true,
+  "description": "Test query_results_cache_compare compares cached results for a query across databases"
+}

client/integration-tests/primitives/tools/query_results_cache_compare/compare_across_databases/test-config.json

@@ -0,0 +1,6 @@
+{
+  "toolName": "query_results_cache_compare",
+  "arguments": {
+    "queryName": "CallGraphFrom"
+  }
+}

client/integration-tests/primitives/tools/query_results_cache_lookup/lookup_by_query_name/after/monitoring-state.json

@@ -0,0 +1,9 @@
+{
+  "toolName": "query_results_cache_lookup",
+  "parameters": {
+    "queryName": "PrintAST",
+    "language": "javascript"
+  },
+  "success": true,
+  "description": "Successfully looked up cached query results by query name and language"
+}

client/integration-tests/primitives/tools/query_results_cache_lookup/lookup_by_query_name/before/monitoring-state.json

@@ -0,0 +1,9 @@
+{
+  "toolName": "query_results_cache_lookup",
+  "parameters": {
+    "queryName": "PrintAST",
+    "language": "javascript"
+  },
+  "expectedSuccess": true,
+  "description": "Test query_results_cache_lookup lists cached results by query name and language"
+}

client/integration-tests/primitives/tools/query_results_cache_lookup/lookup_by_query_name/test-config.json

@@ -0,0 +1,7 @@
+{
+  "toolName": "query_results_cache_lookup",
+  "arguments": {
+    "queryName": "PrintAST",
+    "language": "javascript"
+  }
+}

client/integration-tests/primitives/tools/query_results_cache_retrieve/retrieve_with_subset/after/monitoring-state.json

@@ -0,0 +1,9 @@
+{
+  "toolName": "query_results_cache_retrieve",
+  "parameters": {
+    "cacheKey": "nonexistent-key-for-test",
+    "maxLines": 50
+  },
+  "success": true,
+  "description": "Successfully handled cache retrieve for non-existent key"
+}