docs: Updated the docs to mention that installing the bundled MCP config merges configs now, not overwrites the old one

MCP-Servers.md

@@ -252,11 +252,10 @@ Coyote ships with a `functions/mcp.json` file that includes some useful MCP serv
   graph. The server is rooted at the directory Coyote is launched from (`--project .`), runs fully locally (no network access needed),
   and requires the `iwec` binary. Pairs with the built-in `iwe-knowledge-base` [skill](Skills), which enables this server on load.
 
-The `mcp.json` file is created from a bundled template on first run and is never overwritten afterward. It is your own
+The `mcp.json` file is created from a bundled template on first run. It is your own configuration to edit freely.
-configuration to edit freely. To discard your changes and restore the bundled template (for example, to pick up new
+To pick up new default servers added in a Coyote update, run `coyote --install mcp_config` (or `.install mcp_config`
-default servers after a Coyote update), run `coyote --install mcp_config` (or `.install mcp_config` in the REPL). **This is
+in the REPL). This **merges** the bundled template into your existing configuration: only servers not already present
-destructive:** it replaces your entire `mcp.json`, including your configured servers and any secret references in them,
+in your file are added; your existing servers and any custom secret references are left untouched.
-with the bundled template.
 
 # Coyote Configuration
 MCP servers, like tools, can be used in a handful of contexts:

REPL.md

@@ -265,21 +265,21 @@ command force-overwrites a category of bundled assets with the versions packaged
 when an update ships improved built-ins you want to adopt.
 
 | Command               | Description                                                                    |
-|-----------------------|----------------------------------------------------------------------|
+|-----------------------|--------------------------------------------------------------------------------|
 | `.install agents`     | Reinstall the built-in agents                                                  |
 | `.install macros`     | Reinstall the built-in macros                                                  |
 | `.install skills`     | Reinstall the built-in skills                                                  |
 | `.install functions`  | Reinstall the built-in tool functions (leaves your `mcp.json` alone)           |
-| `.install mcp_config` | Replace `mcp.json` with the bundled template (see warning below)     |
+| `.install mcp_config` | Merge new bundled MCP servers into `mcp.json` (existing servers are preserved) |
 
 The same operation is available from the command line: `coyote --install <category>` (e.g. `coyote --install agents`).
 
 `.install` prompts for confirmation before overwriting anything. Assets you created yourself are never touched. Only
 Coyote's own bundled assets are replaced.
 
-**Warning:** `.install mcp_config` is destructive in a way the others are not. It replaces your entire `mcp.json`
+`.install mcp_config` merges the bundled MCP server list into your existing `mcp.json`. Only servers not already
-(your configured MCP servers and any secret references in them) with Coyote's bundled template. The other categories
+present in your file are added; your existing servers and any custom secret references are left untouched. This
-only overwrite Coyote's built-in assets and leave your custom ones alone.
+behaves consistently with the other install categories, which also leave your own customizations alone.
 
 ## `.install remote` - Install assets from a git repository