Add a new prompt & tool for diagnosing FPs/FNs from query runs.

client/integration-tests/primitives/tools/read_database_source/list_source_files/README.md

@@ -0,0 +1,17 @@
+# `read_database_source` - list_source_files
+
+## Purpose
+
+Tests the `read_database_source` tool in listing mode by omitting `filePath` to list all source files in a CodeQL database source archive.
+
+## Inputs
+
+- **database**: Path to the JavaScript example test database
+
+## Expected Behavior
+
+The tool should return a listing of all source files in the database's `src/` directory, including `totalEntries`, `returnedEntries`, and `truncated` metadata.
+
+## Static Files Referenced
+
+- `server/ql/javascript/examples/test/ExampleQuery1/ExampleQuery1.testproj`

client/integration-tests/primitives/tools/read_database_source/list_source_files/after/monitoring-state.json

@@ -0,0 +1,14 @@
+{
+  "sessions": [
+    {
+      "id": "integration_test_session",
+      "calls": [
+        {
+          "tool": "read_database_source",
+          "timestamp": "2025-09-25T16:06:00.000Z",
+          "status": "success"
+        }
+      ]
+    }
+  ]
+}

client/integration-tests/primitives/tools/read_database_source/list_source_files/before/monitoring-state.json

@@ -0,0 +1,6 @@
+{
+  "sessions": [],
+  "parameters": {
+    "databasePath": "server/ql/javascript/examples/test/ExampleQuery1/ExampleQuery1.testproj"
+  }
+}

client/integration-tests/primitives/tools/read_database_source/read_source_file/README.md

@@ -0,0 +1,18 @@
+# `read_database_source` - read_source_file
+
+## Purpose
+
+Tests the `read_database_source` tool in file-read mode by requesting a specific source file from a CodeQL database source archive.
+
+## Inputs
+
+- **database**: Path to the JavaScript example test database
+- **filePath**: Path to a source file within the database archive
+
+## Expected Behavior
+
+The tool should return the contents of the requested source file along with metadata including `entryPath`, `sourceType`, `totalLines`, `startLine`, and `endLine`.
+
+## Static Files Referenced
+
+- `server/ql/javascript/examples/test/ExampleQuery1/ExampleQuery1.testproj`

client/integration-tests/primitives/tools/read_database_source/read_source_file/after/monitoring-state.json

@@ -0,0 +1,14 @@
+{
+  "sessions": [
+    {
+      "id": "integration_test_session",
+      "calls": [
+        {
+          "tool": "read_database_source",
+          "timestamp": "2025-09-25T16:06:00.000Z",
+          "status": "success"
+        }
+      ]
+    }
+  ]
+}

client/integration-tests/primitives/tools/read_database_source/read_source_file/before/monitoring-state.json

@@ -0,0 +1,7 @@
+{
+  "sessions": [],
+  "parameters": {
+    "databasePath": "server/ql/javascript/examples/test/ExampleQuery1/ExampleQuery1.testproj",
+    "filePath": "ExampleQuery1.js"
+  }
+}

docs/ql-mcp/prompts.md

@@ -4,22 +4,23 @@
 
 ## Overview
 
-The server provides **10 prompts** that guide AI assistants through common CodeQL development workflows. Each prompt is backed by a `*.prompt.md` file containing structured instructions.
+The server provides **11 prompts** that guide AI assistants through common CodeQL development workflows. Each prompt is backed by a `*.prompt.md` file containing structured instructions.
 
 ## Prompt Reference
 
-| Prompt                         | Description                                                                                                          |
-| ------------------------------ | -------------------------------------------------------------------------------------------------------------------- |
-| `document_codeql_query`        | Create or update documentation for a CodeQL query                                                                    |
-| `explain_codeql_query`         | Generate a detailed explanation of a CodeQL query for workshop learning content                                      |
-| `ql_lsp_iterative_development` | Iterative CodeQL query development using LSP tools for completion, navigation, and validation                        |
-| `ql_tdd_advanced`              | Advanced test-driven CodeQL development with AST visualization, control flow, and call graph analysis                |
-| `ql_tdd_basic`                 | Test-driven CodeQL query development checklist — write tests first, implement query, iterate until tests pass        |
-| `sarif_rank_false_positives`   | Analyze SARIF results to identify likely false positives in CodeQL query results                                     |
-| `sarif_rank_true_positives`    | Analyze SARIF results to identify likely true positives in CodeQL query results                                      |
-| `test_driven_development`      | Test-driven development workflow for CodeQL queries using MCP tools                                                  |
-| `tools_query_workflow`         | Guide for using built-in tools queries (PrintAST, PrintCFG, CallGraphFrom, CallGraphTo) to understand code structure |
-| `workshop_creation_workflow`   | Guide for creating CodeQL query development workshops from production-grade queries                                  |
+| Prompt                                    | Description                                                                                                          |
+| ----------------------------------------- | -------------------------------------------------------------------------------------------------------------------- |
+| `document_codeql_query`                   | Create or update documentation for a CodeQL query                                                                    |
+| `explain_codeql_query`                    | Generate a detailed explanation of a CodeQL query for workshop learning content                                      |
+| `ql_lsp_iterative_development`            | Iterative CodeQL query development using LSP tools for completion, navigation, and validation                        |
+| `ql_tdd_advanced`                         | Advanced test-driven CodeQL development with AST visualization, control flow, and call graph analysis                |
+| `ql_tdd_basic`                            | Test-driven CodeQL query development checklist — write tests first, implement query, iterate until tests pass        |
+| `run_query_and_summarize_false_positives` | Run a CodeQL query and summarize its false positives                                                                 |
+| `sarif_rank_false_positives`              | Analyze SARIF results to identify likely false positives in CodeQL query results                                     |
+| `sarif_rank_true_positives`               | Analyze SARIF results to identify likely true positives in CodeQL query results                                      |
+| `test_driven_development`                 | Test-driven development workflow for CodeQL queries using MCP tools                                                  |
+| `tools_query_workflow`                    | Guide for using built-in tools queries (PrintAST, PrintCFG, CallGraphFrom, CallGraphTo) to understand code structure |
+| `workshop_creation_workflow`              | Guide for creating CodeQL query development workshops from production-grade queries                                  |
 
 ## Prompt Categories
 
@@ -41,6 +42,7 @@ The server provides **10 prompts** that guide AI assistants through common CodeQ
 ### Documentation and Quality
 
 - **`document_codeql_query`** — Generates standardized markdown documentation as a sibling file to a query.
+- **`run_query_and_summarize_false_positives`** — Runs a CodeQL query on a database and groups results into false-positive categories by root cause.
 - **`sarif_rank_false_positives`** / **`sarif_rank_true_positives`** — Help assess query precision by ranking SARIF results.
 
 ### Workshop Creation

extensions/vscode/test/fixtures/multi-root-workspace/folder-a/codeql-storage/queries/SqlInjection.ql-def456/query.log

@@ -0,0 +1,2 @@
+[2026-01-20 15:00:00] [SPAMMY] execute query-server2> runQuery called with /workspace/src/SqlInjection.ql
+[2026-01-20 15:00:01] Calling plumbing command: codeql resolve upgrades --dbscheme=/databases/test-python-db/db-python/semmlecode.python.dbscheme --format=json