From af91b89cff13fcafd29d52be71ed03b82705bbf8 Mon Sep 17 00:00:00 2001
From: Alex Clarke <alex.j.tusa@gmail.com>
Date: Mon, 6 Jul 2026 09:57:17 -0600
Subject: [PATCH] feat: merge MCP config when installing bundled mcp config

---
 src/config/mod.rs             |  7 ++++---
 src/config/request_context.rs | 19 ++++++++++++------
 src/function/mod.rs           | 38 ++++++++++++++++++++++++++++++-----
 3 files changed, 50 insertions(+), 14 deletions(-)

diff --git a/src/config/mod.rs b/src/config/mod.rs
index 4d9eb06..3a0e05a 100644
--- a/src/config/mod.rs
+++ b/src/config/mod.rs
@@ -445,9 +445,10 @@ fn confirm_asset_overwrite(category: AssetCategory, label: &str, target: &Path)
     }
     let body = match category {
         AssetCategory::McpConfig => format!(
-            "This replaces your MCP server configuration at {} with this \
-             build's bundled template. Your configured MCP servers (and any \
-             custom secret references they contain) will be lost.",
+            "This merges the bundled MCP server template into your configuration \
+             at {}. New servers from the bundled template will be added; any \
+             MCP servers you have already configured (including custom secret \
+             references) are left untouched.",
             target.display()
         ),
         _ => format!(
diff --git a/src/config/request_context.rs b/src/config/request_context.rs
index 320e644..187cef7 100644
--- a/src/config/request_context.rs
+++ b/src/config/request_context.rs
@@ -5175,19 +5175,26 @@ mod tests {
 
     #[test]
     #[serial]
-    fn install_mcp_config_overwrites_existing() {
+    fn install_mcp_config_merges_existing() {
         let _guard = TestConfigDirGuard::new();
 
         Functions::install_mcp_config().unwrap();
         let mcp = paths::mcp_config_file();
         assert!(mcp.exists(), "install_mcp_config should create mcp.json");
 
-        write(&mcp, "USER_MCP_CONFIG").unwrap();
+        let custom_json =
+            r#"{"mcpServers":{"my-custom-server":{"type":"stdio","command":"custom-cmd"}}}"#;
+        write(&mcp, custom_json).unwrap();
         Functions::install_mcp_config().unwrap();
-        assert_ne!(
-            read_to_string(&mcp).unwrap(),
-            "USER_MCP_CONFIG",
-            "install_mcp_config must overwrite the existing mcp.json"
+
+        let result = read_to_string(&mcp).unwrap();
+        assert!(
+            result.contains("my-custom-server"),
+            "install_mcp_config must preserve user-added MCP servers"
+        );
+        assert!(
+            result.contains("github"),
+            "install_mcp_config must add new bundled servers"
         );
     }
 }
diff --git a/src/function/mod.rs b/src/function/mod.rs
index 4fe1ce5..3d79356 100644
--- a/src/function/mod.rs
+++ b/src/function/mod.rs
@@ -14,7 +14,7 @@ use crate::config::ensure_parent_exists;
 use crate::config::paths;
 use crate::mcp::{
     MCP_DESCRIBE_META_FUNCTION_NAME_PREFIX, MCP_INVOKE_META_FUNCTION_NAME_PREFIX,
-    MCP_SEARCH_META_FUNCTION_NAME_PREFIX,
+    MCP_SEARCH_META_FUNCTION_NAME_PREFIX, McpServersConfig,
 };
 use crate::parsers::{bash, python, typescript};
 use anyhow::{Context, Result, anyhow, bail};
@@ -266,14 +266,42 @@ impl Functions {
         let file_path = paths::mcp_config_file();
         let embedded = FunctionAssets::get("mcp.json")
             .ok_or_else(|| anyhow!("Failed to load embedded mcp.json"))?;
-        let content = unsafe { std::str::from_utf8_unchecked(&embedded.data) };
+        let bundled_content = unsafe { std::str::from_utf8_unchecked(&embedded.data) };
+        let bundled: McpServersConfig =
+            serde_json::from_str(bundled_content).context("failed to parse embedded mcp.json")?;
 
         ensure_parent_exists(&file_path)?;
 
-        info!("Reinstalling MCP config file: {}", file_path.display());
+        let mut merged = if file_path.exists() {
+            let existing =
+                fs::read_to_string(&file_path).context("failed to read existing mcp.json")?;
+            serde_json::from_str::<McpServersConfig>(&existing)
+                .context("failed to parse existing mcp.json")?
+        } else {
+            McpServersConfig {
+                mcp_servers: IndexMap::new(),
+            }
+        };
 
-        let mut config_file = File::create(&file_path)?;
-        config_file.write_all(content.as_bytes())?;
+        let mut added = Vec::new();
+        for (name, server) in bundled.mcp_servers {
+            if !merged.mcp_servers.contains_key(&name) {
+                merged.mcp_servers.insert(name.clone(), server);
+                added.push(name);
+            }
+        }
+
+        info!("Merging bundled MCP config into: {}", file_path.display());
+
+        let serialized =
+            serde_json::to_string_pretty(&merged).context("failed to serialize merged mcp.json")?;
+        let tmp = file_path.with_extension("json.tmp");
+        fs::write(&tmp, &serialized).context("failed to write temporary mcp.json")?;
+        fs::rename(&tmp, &file_path).context("failed to finalize mcp.json")?;
+
+        if !added.is_empty() {
+            println!("  + new MCP servers: {}", added.join(", "));
+        }
 
         Ok(())
     }