Enhance initialization and API handling

- Updated the `InitCommand` to conditionally add and commit all changes after initializing a git repository, improving project setup efficiency.
- Modified the API service to include requested IDs in the instance retrieval process, ensuring accurate instance management.

These changes aim to streamline the initialization process and enhance the API's functionality for better user experience.

src/web/api.rs

@@ -3411,6 +3411,12 @@ impl ApiService {
                 }
             }
 
+            for &id in &requested_ids {
+                if tree.get_instance(id).is_some() {
+                    included_ids.insert(id);
+                }
+            }
+
             for &id in &included_ids {
                 if let Some(instance) = tree.get_instance(id) {
                     instances.insert(id, instance_for_scripts_only(instance, &included_ids));