feat: prefer ~/.config/coyote/mcp.json for the user-scope MCP config

The user-scope MCP config historically lived at
<config-dir>/functions/mcp.json, a leftover from when MCP support was
part of the llm-functions tooling. It now resolves through a single
choke point with these semantics:

- Preferred location: <config-dir>/mcp.json (created there on first run)
- Historical <config-dir>/functions/mcp.json still honored when the
  preferred file does not exist, so existing installs are unchanged
- If both exist, the preferred location wins

--info/.info now reports the resolved location as mcp_config_file, and
the --scope help text plus config.agent.example.yaml reference the new
default. This also removes the asymmetry with the workspace scope,
which already used .coyote/mcp.json directly.

config.agent.example.yaml

@@ -48,7 +48,7 @@ summarization_model: null        # Model to use for summarizing sub-agent output
 summarization_threshold: 4000    # Character threshold above which sub-agent output is summarized before returning to parent
 escalation_timeout: 300          # Seconds a sub-agent waits for a user interaction response before timing out (default: 5 minutes)
 mcp_servers:                     # Optional list of MCP servers that the agent utilizes
-  - github                       # Corresponds to the name of an MCP server in the `<coyote-config-dir>/functions/mcp.json` file
+  - github                       # Corresponds to the name of an MCP server in the `<coyote-config-dir>/mcp.json` file
 global_tools:                    # Optional list of additional global tools to enable for the agent; i.e. not tools specific to the agent
   - web_search
   - fs