Improve ql-mcp-client from PR feedback

Author: data-douser

.github/agents/ql-agent-skills-developer.md

@@ -35,6 +35,22 @@ Get the current list of all tools available in the CodeQL Development MCP Server
 gh-ql-mcp-client list tools --format json
 ```
 
+### List QL MCP Server Prompts
+
+Get the current list of all prompts available in the CodeQL Development MCP Server:
+
+```sh
+gh-ql-mcp-client list prompts --format json
+```
+
+### List QL MCP Server Resources
+
+Get the current list of all resources available in the CodeQL Development MCP Server:
+
+```sh
+gh-ql-mcp-client list resources --format json
+```
+
 ## References
 
 - [`.github/skills/README.md`](../skills/README.md)

.github/workflows/client-integration-tests.yml

@@ -36,7 +36,6 @@ jobs:
         os: [ubuntu-latest, windows-latest]
 
     env:
-      ENABLE_ANNOTATION_TOOLS: 'true'
       HTTP_HOST: 'localhost'
       HTTP_PORT: '3000'
       MCP_MODE: ${{ matrix.mcp-mode }}

client/CLI-USAGE.md

@@ -1,6 +1,6 @@
 # gh-ql-mcp-client CLI Usage Guide
 
-This document describes how to use the `gh-ql-mcp-client` CLI for Code Scanning alert lifecycle management and MCP server integration testing.
+This document describes how to use the `gh-ql-mcp-client` CLI for MCP server integration testing and MCP primitive listing.
 
 ## Overview
 
@@ -15,84 +15,42 @@ gh ql-mcp-client <command> [flags]
 
 # Help for any command
 gh-ql-mcp-client --help
-gh-ql-mcp-client code-scanning --help
-gh-ql-mcp-client code-scanning list-alerts --help
+gh-ql-mcp-client list --help
+gh-ql-mcp-client integration-tests --help
 ```
 
 ## Commands
 
-### `code-scanning` (alias: `cs`)
+### `list`
 
-Interact with the GitHub Code Scanning REST API. Requires `gh` CLI authentication.
+List MCP server primitives (tools, prompts, resources).
 
-#### `list-analyses`
+#### `list tools`
 
-List Code Scanning analyses for a repository.
+List all tools registered on the MCP server.
 
 ```bash
-gh-ql-mcp-client code-scanning list-analyses --repo owner/repo
-gh-ql-mcp-client cs list-analyses --repo owner/repo --tool-name CodeQL --ref refs/heads/main
-gh-ql-mcp-client cs list-analyses --repo owner/repo --format json
+gh-ql-mcp-client list tools
+gh-ql-mcp-client list tools --format json
+gh-ql-mcp-client list tools --mode http --port 3000
 ```
 
-**Flags:**
-
-| Flag          | Description                                  |
-| ------------- | -------------------------------------------- |
-| `--repo`      | Repository in `owner/repo` format (required) |
-| `--ref`       | Git ref to filter by                         |
-| `--tool-name` | Tool name to filter by (e.g. `CodeQL`)       |
-| `--sarif-id`  | SARIF ID to filter by                        |
-| `--sort`      | Sort by (`created`)                          |
-| `--direction` | Sort direction (`asc`, `desc`)               |
-| `--per-page`  | Results per page (default: 30, max: 100)     |
-
-#### `list-alerts`
-
-List Code Scanning alerts for a repository.
-
-```bash
-gh-ql-mcp-client code-scanning list-alerts --repo owner/repo
-gh-ql-mcp-client cs list-alerts --repo owner/repo --state open --severity high
-gh-ql-mcp-client cs list-alerts --repo owner/repo --tool-name CodeQL --format json
-```
-
-**Flags:**
-
-| Flag          | Description                                                      |
-| ------------- | ---------------------------------------------------------------- |
-| `--repo`      | Repository in `owner/repo` format (required)                     |
-| `--ref`       | Git ref to filter by                                             |
-| `--state`     | Alert state: `open`, `closed`, `dismissed`, `fixed`              |
-| `--severity`  | Severity: `critical`, `high`, `medium`, `low`, `warning`, `note` |
-| `--tool-name` | Tool name to filter by                                           |
-| `--sort`      | Sort by (`created`, `updated`)                                   |
-| `--direction` | Sort direction (`asc`, `desc`)                                   |
-| `--per-page`  | Results per page (default: 30, max: 100)                         |
+#### `list prompts`
 
-#### `download-analysis`
-
-Download a Code Scanning analysis as SARIF.
+List all prompts registered on the MCP server.
 
 ```bash
-gh-ql-mcp-client code-scanning download-analysis --repo owner/repo --analysis-id 12345
-gh-ql-mcp-client cs download-analysis --repo owner/repo --analysis-id 12345 --output my-results.sarif
+gh-ql-mcp-client list prompts
+gh-ql-mcp-client list prompts --format json
 ```
 
-**Flags:**
-
-| Flag            | Description                                                             |
-| --------------- | ----------------------------------------------------------------------- |
-| `--repo`        | Repository in `owner/repo` format (required)                            |
-| `--analysis-id` | Analysis ID to download (required)                                      |
-| `--output`      | Output file path (default: `sarif-downloads/<owner>_<repo>/<id>.sarif`) |
-
-### `sarif`
+#### `list resources`
 
-SARIF analysis and alert comparison tools. These commands delegate to MCP server tools.
+List all resources registered on the MCP server.
 
 ```bash
-gh-ql-mcp-client sarif --help
+gh-ql-mcp-client list resources
+gh-ql-mcp-client list resources --format json
 ```
 
 ### `integration-tests`
@@ -129,11 +87,13 @@ These flags are available on all commands:
 
 | Flag       | Default     | Description                           |
 | ---------- | ----------- | ------------------------------------- |
-| `--mode`   | `http`      | MCP server transport (`stdio`/`http`) |
+| `--mode`   | `stdio`     | MCP server transport (`stdio`/`http`) |
 | `--host`   | `localhost` | MCP server host (http mode)           |
 | `--port`   | `3000`      | MCP server port (http mode)           |
 | `--format` | `text`      | Output format (`text`/`json`)         |
 
+Transport mode is controlled by the `--mode` flag, which defaults to `stdio`.
+
 ## Integration with Shell Scripts
 
 The `client/scripts/run-integration-tests.sh` script builds the Go binary, starts the MCP server, and runs integration tests:
@@ -155,8 +115,7 @@ The `client/scripts/run-integration-tests.sh` script builds the Go binary, start
 | ----------------- | ------------------------------------------------------- | ---------------------------- |
 | `MCP_SERVER_URL`  | Override MCP server URL (http mode)                     | `http://localhost:3000/mcp`  |
 | `MCP_SERVER_PATH` | Override path to MCP server JS entry point (stdio mode) | Auto-detected from repo root |
-| `MCP_MODE`        | Transport mode (`stdio`/`http`)                         | `http`                       |
-| `HTTP_HOST`       | Server host                                             | `localhost`                  |
-| `HTTP_PORT`       | Server port                                             | `3000`                       |
+
+Transport mode is controlled by the `--mode` flag (default: `stdio`). `MCP_SERVER_URL` is only used to override the server URL when running in `http` mode.
 
 Cobra provides built-in help and validation for all flags. Use `--help` on any command for details.

client/Makefile

@@ -25,7 +25,7 @@ test-unit:
 
 ## test-integration: Build binary and run integration tests via run-integration-tests.sh
 test-integration: build
-	ENABLE_ANNOTATION_TOOLS=true scripts/run-integration-tests.sh --no-install-packs
+	scripts/run-integration-tests.sh --no-install-packs
 
 ## test-verbose: Run all unit tests with verbose output
 test-verbose:

client/README.md

@@ -1,6 +1,6 @@
 # gh-ql-mcp-client
 
-A Go CLI for managing Code Scanning alert lifecycles, combining GitHub's Code Scanning REST API (via `gh` auth) with the CodeQL Development MCP Server's SARIF analysis tools.
+A Go CLI for listing MCP server primitives, running MCP server integration tests, and (planned) managing Code Scanning alert lifecycles.
 
 Installable as a standalone binary or as a `gh` CLI extension (`gh ql-mcp-client`).
 
@@ -42,27 +42,20 @@ Transport is configured via CLI flags. The CLI does not currently read `MCP_MODE
 
 ### Commands
 
-#### `code-scanning` (alias: `cs`)
+#### `list`
 
-Interact with the GitHub Code Scanning REST API.
+List MCP server primitives (tools, prompts, resources).
 
 ```bash
-# List analyses for a repository
-gh-ql-mcp-client code-scanning list-analyses --repo owner/repo
+# List all tools registered on the MCP server
+gh-ql-mcp-client list tools
+gh-ql-mcp-client list tools --format json
 
-# List alerts with filters
-gh-ql-mcp-client code-scanning list-alerts --repo owner/repo --state open --severity high
+# List all prompts
+gh-ql-mcp-client list prompts
 
-# Download a SARIF analysis
-gh-ql-mcp-client code-scanning download-analysis --repo owner/repo --analysis-id 12345
-```
-
-#### `sarif`
-
-SARIF analysis and alert comparison tools (delegates to MCP server tools).
-
-```bash
-gh-ql-mcp-client sarif --help
+# List all resources
+gh-ql-mcp-client list resources
 ```
 
 #### `integration-tests`
@@ -96,9 +89,8 @@ make test-coverage   # Unit tests with coverage report
 | ----------------- | ------------------------------------------------------- | ---------------------------- |
 | `MCP_SERVER_URL`  | Override MCP server URL (http mode)                     | `http://localhost:3000/mcp`  |
 | `MCP_SERVER_PATH` | Override path to MCP server JS entry point (stdio mode) | Auto-detected from repo root |
-| `MCP_MODE`        | Transport mode (`stdio`/`http`)                         | `http`                       |
-| `HTTP_HOST`       | Server host                                             | `localhost`                  |
-| `HTTP_PORT`       | Server port                                             | `3000`                       |
+
+Transport mode is controlled by the `--mode` flag, which defaults to `stdio`. `MCP_SERVER_URL` is only used to override the server URL when running in `http` mode.
 
 ## Architecture
 
@@ -107,15 +99,14 @@ client/
 ├── main.go                     # Entry point
 ├── cmd/                        # Cobra CLI commands
 │   ├── root.go                 # Root command + global flags
-│   ├── code_scanning.go        # code-scanning subcommand group
-│   ├── code_scanning_*.go      # Individual code-scanning subcommands
-│   ├── sarif.go                # sarif subcommand group
+│   ├── list.go                 # list subcommand group (tools/prompts/resources)
+│   ├── helpers.go              # Shared CLI helpers
 │   └── integration_tests.go    # integration-tests command
 ├── internal/
-│   ├── github/                 # GitHub Code Scanning REST API client (via go-gh)
 │   ├── mcp/                    # MCP server client (via mcp-go)
 │   └── testing/                # Integration test runner and parameter builder
 ├── integration-tests/          # Test fixtures (before/after directories)
+├── scripts/                    # Shell scripts for test orchestration
 ├── Makefile                    # Build, test, lint, cross-compile targets
 └── go.mod                      # Go module definition
 ```

client/cmd/integration_tests.go

@@ -136,7 +136,11 @@ func runIntegrationTests(cmd *cobra.Command, _ []string) error {
 	allPassed, _ := runner.Run()
 
 	// Close the MCP client (and its stdio subprocess) before returning.
-	client.Close()
+	// The close may time out for stdio servers (Node.js doesn't always
+	// exit promptly) — log but don't fail the test run for this.
+	if err := client.Close(); err != nil {
+		fmt.Fprintf(os.Stderr, "warning: %v\n", err)
+	}
 
 	if !allPassed {
 		return fmt.Errorf("some integration tests failed")