Edit specialized READMEs

Changes to be committed:
	modified:   templates/README.md
	modified:   tests/README.md

Author: ndaelman-hu

templates/README.md

@@ -1,35 +1,97 @@
 # MCP Configuration Templates
 
-This folder contains MCP server configuration templates for different editors and clients.
-
 ## Quick Setup
 
-### VS Code (verified)
-1. Copy `vscode-mcp.json` to `.vscode/mcp.json` in your project root
-2. Start the server either directly from the file (toggles appear above the server name) or the Extensions icon (right-click on the server)
+Ready-to-use configuration templates are available in the `templates/` folder:
+
+- **VS Code**: Copy `templates/vscode-mcp.json` to `.vscode/mcp.json`
+- **Claude Desktop**: Copy content from `templates/claude-desktop-mcp.json` to your Claude config
+- **Neovim**: Use `templates/neovim-mcp.json` as a starting point
+
+### Individual Servers (Testing)
+
+For testing specific parsers, you can add individual server configurations, based on the example templates, provided.
+Here is an example for VS Code:
+
+```json
+{
+  "servers": {
+    "parse-patrol": {
+      "command": "uv",
+      "args": ["run", "python", "-m", "parse_patrol"],
+      "cwd": "/path/to/parse-patrol"
+    },
+    "parse-patrol-cclib": {
+      "command": "uv", 
+      "args": ["run", "python", "-m", "parse_patrol.parsers.cclib"],
+      "cwd": "/path/to/parse-patrol"
+    },
+    "parse-patrol-nomad": {
+      "command": "uv",
+      "args": ["run", "python", "-m", "parse_patrol.databases.nomad"],
+      "cwd": "/path/to/parse-patrol"
+    }
+  }
+}
+```
+
+## VS Code (verified)
+
+### Starting the Server
+
+#### Locally
+
+1. Copy `vscode-mcp.json` to `.vscode/mcp.json` in your project root.
+2. Start the server either directly from the file (toggles appear above the server name) or the Extensions icon (right-click on the server for all options).
 3. Use Agent mode in Copilot Chat to access parse-patrol tools
 
+![mcp.json](assets/images/mcp_json.png)
+
+#### Remotely
+
+In VS Code, go to the command prompt, type `> mcp` and select "MCP: Open Remote User Configuration".
+It will open up a `mcp.json` file, where you can paste in your MCP server configurations.
+
+### Using the Agent
+
+Once the server is started, it will be available under the `CHAT` tab when running `Agent` mode.
+Note that the default mode for co-pilot is `Ask/Edit` mode.
+
+To access *resources* type the pound symbol (`#`), for prompt commands type slash (`/`) in the chat window and wait for auto-complete.
+All resources and prompts names should start with `mcp.parse-patrol`.
+(Note that the MCP server name may change when published under a different or multiple servers.)
+
+When executing a prompt command, the input parameters will pop up at the top.
+Their names and descriptions are outlined above the active text bar.
+Input parameters may be required or optional (marked as such) input.
+In the case of the later, the field can be left blank.
+Finally, the full prompt will be returned to the chat input field, ready to be submitted.
+Reviewing or editing is still possible at this step.
+
+PITFALL: do not use the file explorer for adding fields, but the resource dialog.
+Else you copy-paste the file contents, NOT the file path.
+
 ### Claude Desktop (experimental)
 
-**Option 1: Project-scoped (Recommended)**
+**Option 1: Project-scoped (Recommended):**
+
 ```bash
 # From your parse-patrol project directory
 # First ensure dependencies are installed
 uv sync --extra mcp
 
 # Add the MCP server - use absolute path to ensure correct environment
 claude mcp add parse-patrol --scope project -- sh -c "cd $(pwd) && PYTHONPATH=src uv --project $(pwd) run python -m parse_patrol"
-
-# Alternative: Use the venv python directly
-# claude mcp add parse-patrol --scope project -- sh -c "cd $(pwd) && PYTHONPATH=src $(pwd)/.venv/bin/python -m parse_patrol"
 ```
 
 **Environment Issues:**
+
 - The `claude mcp add` command may run in a different `uv` environment than your project
 - Using `--project $(pwd)` ensures `uv` uses the correct project environment
 - Alternatively, use the venv Python directly: `.venv/bin/python`
 
-**Option 2: Manual configuration**
+**Option 2: Manual configuration:**
+
 1. Copy `claude-desktop-mcp.json` content to your Claude Desktop configuration file:
    - **macOS**: `~/Library/Application Support/Claude/claude_desktop_config.json`
    - **Windows**: `%APPDATA%\Claude\claude_desktop_config.json`
@@ -38,6 +100,7 @@ claude mcp add parse-patrol --scope project -- sh -c "cd $(pwd) && PYTHONPATH=sr
 3. Restart Claude Desktop
 
 **Troubleshooting Claude MCP:**
+
 - **Environment mismatch**: If "No module named 'mcp'" error, the `uv` environment differs from your project
   - Use `uv --project $(pwd) run` or direct venv path: `.venv/bin/python`
   - Test manually: `cd /your/project && PYTHONPATH=src uv run python -m parse_patrol`
@@ -46,48 +109,21 @@ claude mcp add parse-patrol --scope project -- sh -c "cd $(pwd) && PYTHONPATH=sr
   - Verify imports work: `PYTHONPATH=src uv run python -c "import parse_patrol.__main__"`
 - **Server doesn't sync**: Try restarting Claude Desktop after adding the server
 
-### Neovim (with MCP support) (experimental)
+### Neovim (experimental)
+
 1. Copy `neovim-mcp.json` to your Neovim MCP configuration location
 2. Configure according to your MCP plugin requirements
 
 ## Configuration Options
 
 ### Main Server (Recommended)
+
 All templates use the unified server by default, which provides:
-- All parser tools (cclib, gaussian, iodata)
+
+- All parser tools (`cclib`, `iodata`)
 - Database tools (NOMAD search/download)
 - Pre-built prompts for chemistry workflows
 
-### Individual Servers (Testing)
-For testing specific parsers, you can add individual server configurations:
-
-```json
-{
-  "servers": {
-    "parse-patrol": {
-      "command": "uv",
-      "args": ["run", "python", "-m", "parse_patrol"],
-      "cwd": "/path/to/parse-patrol"
-    },
-    "parse-patrol-cclib": {
-      "command": "uv", 
-      "args": ["run", "python", "-m", "parse_patrol.parsers.cclib"],
-      "cwd": "/path/to/parse-patrol"
-    },
-    "parse-patrol-gaussian": {
-      "command": "uv",
-      "args": ["run", "python", "-m", "parse_patrol.parsers.gaussian"],
-      "cwd": "/path/to/parse-patrol"
-    },
-    "parse-patrol-nomad": {
-      "command": "uv",
-      "args": ["run", "python", "-m", "parse_patrol.databases.nomad"],
-      "cwd": "/path/to/parse-patrol"
-    }
-  }
-}
-```
-
 ## Path Configuration
 
 - Replace `"${workspaceFolder}"` with the absolute path to your parse-patrol directory if needed
@@ -108,4 +144,4 @@ uv sync --extra mcp
 1. **"No module named 'mcp'" error**: Install MCP dependencies with `uv sync --extra mcp`
 2. **"No module named parse_patrol" error**: Ensure `PYTHONPATH` is set correctly in the configuration
 3. **Server won't start**: Check that `uv` is installed and the path is correct
-4. **Import errors**: Ensure you're using `uv run python -m parse_patrol` (module syntax) not direct file paths
+4. **Import errors**: Ensure you're using `uv run python -m parse_patrol` (module syntax) not direct file paths