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/cli/init.rs

@@ -127,6 +127,10 @@ impl InitCommand {
             !self.skip_git
         };
 
+        if did_git_init {
+            crate::git::git_add_all_and_commit(&base_path, "Initial commit");
+        }
+
         if !self.skip_rules && did_git_init {
             log::debug!("Adding agent submodules...");
 
@@ -189,10 +193,8 @@ impl InitCommand {
             if !any_failed {
                 println!("Added agent submodules successfully.");
             }
-        }
 
-        if did_git_init {
-            crate::git::git_add_all_and_commit(&base_path, "Initial commit");
+            crate::git::git_add_all_and_commit(&base_path, "Add agent submodules");
         }
 
         println!("Created project successfully.");

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));