Enhance prompts, resources, and tool descriptions based on real-world debugging session

server/src/prompts/data-extension-development.prompt.md

@@ -132,6 +132,8 @@ Validate the model against a real database:
 - If the `.model.yml` lives under `.github/codeql/extensions/` of the consuming repo, you are **done** — Code Scanning will load it on the next analysis.
 - If you authored a reusable model pack and want it to apply across an organization, publish it to GHCR with `codeql pack publish` and configure it under org Code security → Global settings → CodeQL analysis → Model packs.
 
+> **When data extensions aren't enough**: If `subtypes: True` fails to match subclasses (common when the base type is a library stub not present in the database), or the detection logic cannot be expressed as a source/sink/summary tuple, a QL library change (`.qll`) is needed instead. Use the `codeql://prompts/ql-tdd-basic` workflow to develop and test the fix, then contribute it upstream to `github/codeql`.
+
 ## Validation Checklist
 
 - [ ] Correct tuple format for the language (API Graph vs MaD)
@@ -147,3 +149,13 @@ Validate the model against a real database:
 - `codeql://languages/{{language}}/library-modeling` — Language-specific library modeling guide
 - `codeql://templates/security` — Security query templates
 - `codeql://learning/test-driven-development` — TDD workflow for CodeQL queries
+
+## Troubleshooting
+
+| Issue | Likely Cause | Resolution |
+| ----- | ------------ | ---------- |
+| Extension not found by `codeql query run` | `.github/codeql/extensions/` is only auto-loaded by Code Scanning (GitHub Actions), not the CLI | Move `.model.yml` into the pack's `ext/` directory (e.g., `csharp/ql/lib/ext/`) or pass the directory via `--additional-packs` |
+| Stale results after adding/changing `.model.yml` | Compilation cache is returning previously cached results | Use `--no-default-compilation-cache` with a fresh `--compilation-cache=<empty-dir>` to force recompilation |
+| `subtypes: True` not matching subclass methods | The base type only exists as a library stub in the database, not as extracted source | `subtypes` resolution requires the declaring type to be in the database. For framework base types (e.g., `PageModel`, `ControllerBase`) that are only stubs, use a QL-based source/sink class instead of a data extension |
+| Extension loads but produces no findings | Missing link in the source → summary → sink chain | Verify all hops are modeled — a single missing `summaryModel` between source and sink will break the chain |
+| YAML parse error or silent failure | Wrong column count for the extensible predicate | Double-check the exact column count for your language's format (MaD vs API Graph) — extra or missing columns fail silently |

server/src/prompts/ql-tdd-basic.prompt.md

@@ -214,6 +214,7 @@ codeql_test_accept: {
 - ❌ Not using #codeql_lsp_completion to discover available types
 - ❌ Not setting `workspace_uri` when using LSP tools (completions will be empty)
 - ❌ Creating tests that are too complex
+- ❌ Not clearing compilation cache after adding data extensions (stale cached results hide new models)
 - ❌ Ignoring false positives in results
 - ❌ Not refactoring after tests pass
 

server/src/resources/languages/csharp_library_modeling.md

@@ -58,6 +58,13 @@ C# uses a **MaD (Models as Data)** format with **9–10 column tuples** that ide
 | `kind`           | Source/sink/summary kind                                                                        | `"sql-injection"`, `"taint"`                            |
 | `provenance`     | Origin of the model                                                                             | `"manual"`                                              |
 
+### Important: `subtypes` Flag
+
+- `True` — the model applies to the method **and all overrides** in subclasses and implementing classes
+- `False` — only applies to the exact class specified
+
+> **Caveat**: `subtypes: True` requires the base type to be **present in the CodeQL database** as extracted source or a resolved reference. For framework base types that exist only as library stubs (e.g., `Microsoft.AspNetCore.Mvc.RazorPages.PageModel`), subtypes resolution may silently fail to match subclass methods. In these cases, model each concrete class explicitly or implement a QL-based source/sink class instead.
+
 ### Important: C#-Specific Signature Rules
 
 - Type names must be **fully qualified**: `System.String`, not `string`

server/src/tools/codeql/bqrs-decode.ts

@@ -23,7 +23,7 @@ export const codeqlBqrsDecodeTool: CLIToolDefinition = {
   command: 'codeql',
   subcommand: 'bqrs decode',
   inputSchema: {
-    files: z.array(z.string()).describe('BQRS file(s) to decode'),
+    files: z.array(z.string()).describe('Array of BQRS file paths to decode. Pass an array even for a single file, e.g. ["/path/to/results.bqrs"]'),
     output: createCodeQLSchemas.output(),
     format: z.enum(['csv', 'json', 'text', 'bqrs']).optional()
       .describe('Output format: text (human-readable table, default), csv, json (streaming JSON), or bqrs (binary, requires --output)'),

server/src/tools/codeql/quick-evaluate.ts

@@ -60,7 +60,10 @@ export async function quickEvaluate({
 export function registerQuickEvaluateTool(server: McpServer): void {
   server.tool(
     'quick_evaluate',
-    'Quick evaluate either a class or a predicate in a CodeQL query for debugging',
+    'Resolve a class or predicate symbol in a CodeQL query file for quick evaluation. ' +
+      'Locates the symbol position and returns an output path for results. ' +
+      'Note: this tool validates the symbol exists but does not yet execute the evaluation — ' +
+      'use codeql_query_run for full evaluation.',
     {
       file: z.string().describe('Path to the .ql file containing the symbol'),
       db: z.string().describe('Path to the CodeQL database'),

server/src/tools/codeql/register-database.ts

@@ -90,7 +90,9 @@ export async function registerDatabase(dbPath: string): Promise<string> {
 export function registerRegisterDatabaseTool(server: McpServer): void {
   server.tool(
     'register_database',
-    'Register a CodeQL database given a local path to the database directory',
+    'Register a CodeQL database for use by other MCP tools. ' +
+      'Validates that the database directory exists, contains codeql-database.yml, and has source files (src.zip or src/). ' +
+      'Does not persist any session state — acts as a preflight check before using other database tools.',
     {
       db_path: z.string().describe('Path to the CodeQL database directory'),
     },