Fix multiple turn-checkpoints issue (#3063)

- Add -f flag to git tag to allow overwriting existing tags
- Move turn checkpoints to end of list when updating to maintain correct chronological ordering
- Update turn checkpoint after each tool use to point to latest state
- Fix expand functionality to show correct tool checkpoints for each turn

Author: kkashilk

crates/chat-cli/src/cli/chat/checkpoint.rs

@@ -171,8 +171,28 @@ impl CheckpointManager {
             tool_name,
         };
 
-        self.checkpoints.push(checkpoint);
-        self.tag_index.insert(tag.to_string(), self.checkpoints.len() - 1);
+        // Check if checkpoint with this tag already exists
+        if let Some(&existing_idx) = self.tag_index.get(tag) {
+            if is_turn {
+                // For turn checkpoints, always move to the end to maintain correct ordering
+                self.checkpoints.remove(existing_idx);
+
+                // Update all indices in tag_index that are greater than the removed index
+                for (_, index) in self.tag_index.iter_mut() {
+                    if *index > existing_idx {
+                        *index -= 1;
+                    }
+                }
+
+                // Add the updated checkpoint at the end
+                self.checkpoints.push(checkpoint);
+                self.tag_index.insert(tag.to_string(), self.checkpoints.len() - 1);
+            }
+        } else {
+            // Add new checkpoint
+            self.checkpoints.push(checkpoint);
+            self.tag_index.insert(tag.to_string(), self.checkpoints.len() - 1);
+        }
 
         // Cache file stats for this checkpoint
         if let Ok(stats) = self.compute_file_stats(tag) {
@@ -404,7 +424,7 @@ fn stage_commit_tag(shadow_path: &str, work_tree: &Path, message: &str, tag: &st
     }
 
     // Tag
-    let output = run_git(Path::new(shadow_path), None, &["tag", tag])?;
+    let output = run_git(Path::new(shadow_path), None, &["tag", tag, "-f"])?;
     if !output.status.success() {
         bail!(
             "Checkpoint initialization failed: {}",

crates/chat-cli/src/cli/chat/mod.rs

@@ -2321,7 +2321,7 @@ impl ChatSession {
                     };
                     let tag = if has_changes {
                         // Generate tag for this tool use
-                        let tag = format!("{}.{}", manager.current_turn + 1, manager.tools_in_turn + 1);
+                        let tool_tag = format!("{}.{}", manager.current_turn + 1, manager.tools_in_turn + 1);
 
                         // Get tool summary for commit message
                         let is_fs_read = matches!(&tool.tool, Tool::FsRead(_));
@@ -2334,9 +2334,9 @@ impl ChatSession {
                             }
                         };
 
-                        // Create checkpoint
+                        // Create tool checkpoint
                         if let Err(e) = manager.create_checkpoint(
-                            &tag,
+                            &tool_tag,
                             &description,
                             &self.conversation.history().clone(),
                             false,
@@ -2346,7 +2346,23 @@ impl ChatSession {
                             None
                         } else {
                             manager.tools_in_turn += 1;
-                            Some(tag)
+
+                            // Also update/create the turn checkpoint to point to latest state
+                            // This is important so that we create turn-checkpoints even when tools are aborted
+                            let turn_tag = format!("{}", manager.current_turn + 1);
+                            let turn_description = "Turn in progress".to_string();
+
+                            if let Err(e) = manager.create_checkpoint(
+                                &turn_tag,
+                                &turn_description,
+                                &self.conversation.history().clone(),
+                                true,
+                                None,
+                            ) {
+                                debug!("Failed to update turn checkpoint: {}", e);
+                            }
+
+                            Some(tool_tag)
                         }
                     } else {
                         None