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

src/cli/mod.rs

@@ -315,7 +315,7 @@ pub struct Cli {
     /// URL for http/sse MCP server (used with --mcp-add)
     #[arg(long, value_name = "URL", help_heading = "MCP Servers")]
     pub url: Option<String>,
-    /// Scope for MCP config: user (~/.config/coyote/functions/mcp.json) or workspace (./.coyote/mcp.json). Default: user
+    /// Scope for MCP config: user (~/.config/coyote/mcp.json) or workspace (./.coyote/mcp.json). Default: user
     #[arg(long, value_enum, value_name = "SCOPE", help_heading = "MCP Servers")]
     pub scope: Option<McpScopeArg>,
     /// Environment variable for stdio MCP server (repeatable): --env KEY=VALUE

src/config/paths.rs

@@ -287,6 +287,18 @@ pub fn functions_bin_dir() -> PathBuf {
 }
 
 pub fn mcp_config_file() -> PathBuf {
+    let preferred = local_dir(MCP_FILE_NAME);
+    if preferred.exists() {
+        return preferred;
+    }
+    let legacy = legacy_mcp_config_file();
+    if legacy.exists() {
+        return legacy;
+    }
+    preferred
+}
+
+pub fn legacy_mcp_config_file() -> PathBuf {
     functions_dir().join(MCP_FILE_NAME)
 }
 
@@ -837,6 +849,80 @@ mod tests {
         }
     }
 
+    mod user_mcp_resolution {
+        use super::*;
+        use serial_test::serial;
+
+        fn with_config_dir<F: FnOnce(&Path)>(f: F) {
+            let unique = time::SystemTime::now()
+                .duration_since(time::UNIX_EPOCH)
+                .unwrap()
+                .as_nanos();
+            let root = env::temp_dir().join(format!("coyote-user-mcp-test-{unique}"));
+            fs::create_dir_all(root.join(FUNCTIONS_DIR_NAME)).unwrap();
+            let config_env = get_env_name("config_dir");
+            let functions_env = get_env_name("functions_dir");
+            let prev_config = env::var_os(&config_env);
+            let prev_functions = env::var_os(&functions_env);
+            unsafe {
+                env::set_var(&config_env, &root);
+                env::set_var(&functions_env, root.join(FUNCTIONS_DIR_NAME));
+            }
+            f(&root);
+            unsafe {
+                match prev_config {
+                    Some(v) => env::set_var(&config_env, v),
+                    None => env::remove_var(&config_env),
+                }
+                match prev_functions {
+                    Some(v) => env::set_var(&functions_env, v),
+                    None => env::remove_var(&functions_env),
+                }
+            }
+            let _ = fs::remove_dir_all(&root);
+        }
+
+        #[test]
+        #[serial]
+        fn defaults_to_preferred_location_when_neither_exists() {
+            with_config_dir(|root| {
+                assert_eq!(mcp_config_file(), root.join(MCP_FILE_NAME));
+            });
+        }
+
+        #[test]
+        #[serial]
+        fn falls_back_to_legacy_location_when_only_it_exists() {
+            with_config_dir(|root| {
+                let legacy = root.join(FUNCTIONS_DIR_NAME).join(MCP_FILE_NAME);
+                fs::write(&legacy, "{}").unwrap();
+                assert_eq!(mcp_config_file(), legacy);
+            });
+        }
+
+        #[test]
+        #[serial]
+        fn prefers_new_location_when_both_exist() {
+            with_config_dir(|root| {
+                let preferred = root.join(MCP_FILE_NAME);
+                let legacy = root.join(FUNCTIONS_DIR_NAME).join(MCP_FILE_NAME);
+                fs::write(&preferred, "{}").unwrap();
+                fs::write(&legacy, "{}").unwrap();
+                assert_eq!(mcp_config_file(), preferred);
+            });
+        }
+
+        #[test]
+        #[serial]
+        fn uses_preferred_location_when_only_it_exists() {
+            with_config_dir(|root| {
+                let preferred = root.join(MCP_FILE_NAME);
+                fs::write(&preferred, "{}").unwrap();
+                assert_eq!(mcp_config_file(), preferred);
+            });
+        }
+    }
+
     #[test]
     fn sandbox_kit_override_reflects_env_var_state() {
         let env_name = get_env_name("sandbox_kit");

src/config/request_context.rs

@@ -1865,6 +1865,7 @@ impl RequestContext {
             ("rags_dir", display_path(&paths::rags_dir())),
             ("macros_dir", display_path(&paths::macros_dir())),
             ("functions_dir", display_path(&paths::functions_dir())),
+            ("mcp_config_file", display_path(&paths::mcp_config_file())),
             ("sbx_kit_dir", display_path(&paths::sbx_kit_dir())),
             ("messages_file", display_path(&self.messages_file())),
         ];

src/function/mod.rs

@@ -517,7 +517,11 @@ impl Functions {
                 anyhow!("Failed to load embedded function file: {}", file.as_ref())
             })?;
             let content = unsafe { std::str::from_utf8_unchecked(&embedded_file.data) };
-            let file_path = paths::functions_dir().join(file.as_ref());
+            let file_path = if file.as_ref() == "mcp.json" {
+                paths::mcp_config_file()
+            } else {
+                paths::functions_dir().join(file.as_ref())
+            };
             let is_script = file_path
                 .extension()
                 .and_then(OsStr::to_str)