feat(mcp): enhance MCP server registration with error handling and improve transport process management

refactor: update various tools for better error handling and path resolution
fix: improve markdown rendering and input display in TUI

apps/infrastructure/src/utils.rs

@@ -69,31 +69,42 @@ impl CastOr<u32> for u128 {
 
 /// Atomically write serializable `data` to `path`.
 ///
-/// Flow: serialize to pretty JSON -> write to `path.tmp` -> fsync -> rename
+/// Flow: serialize to pretty JSON -> write to `path.tmp.<uuid>` -> fsync -> rename
 /// -> fsync parent. If `mode` is `Some`, set permissions before rename (Unix only).
+///
+/// A UUID-based temporary filename avoids collisions from concurrent writes.
+/// Orphaned tmp files are cleaned up on any error after creation.
 pub fn write_json_atomic<T: Serialize>(path: &Path, data: &T, mode: Option<u32>) -> std::io::Result<()> {
-    let tmp = path.with_extension("tmp");
-    let bytes = serde_json::to_vec_pretty(data)
-        .map_err(|e| std::io::Error::new(std::io::ErrorKind::InvalidData, e))?;
-    {
-        let mut f = std::fs::OpenOptions::new()
-            .create(true)
-            .truncate(true)
-            .write(true)
-            .open(&tmp)?;
-        f.write_all(&bytes)?;
-        f.sync_all()?;
-    }
-    if let Some(m) = mode {
-        #[cfg(unix)]
+    let tmp = path.with_extension(format!("tmp.{}", uuid::Uuid::new_v4()));
+    let result = (|| -> std::io::Result<()> {
+        let bytes = serde_json::to_vec_pretty(data)
+            .map_err(|e| std::io::Error::new(std::io::ErrorKind::InvalidData, e))?;
         {
-            use std::os::unix::fs::PermissionsExt;
-            std::fs::set_permissions(&tmp, std::fs::Permissions::from_mode(m))?;
+            let mut f = std::fs::OpenOptions::new()
+                .create(true)
+                .truncate(true)
+                .write(true)
+                .open(&tmp)?;
+            f.write_all(&bytes)?;
+            f.sync_all()?;
         }
-        #[cfg(not(unix))]
-        { let _ = m; }
+        if let Some(m) = mode {
+            #[cfg(unix)]
+            {
+                use std::os::unix::fs::PermissionsExt;
+                std::fs::set_permissions(&tmp, std::fs::Permissions::from_mode(m))?;
+            }
+            #[cfg(not(unix))]
+            { let _ = m; }
+        }
+        std::fs::rename(&tmp, path)?;
+        Ok(())
+    })();
+    // Clean up orphaned temp file on error after creation
+    if let Err(e) = result {
+        let _ = std::fs::remove_file(&tmp);
+        return Err(e);
     }
-    std::fs::rename(&tmp, path)?;
     if let Some(parent) = path.parent() {
         let _ = std::fs::File::open(parent).and_then(|d| d.sync_all());
     }