fix: improve checkpoint timing logic

- Save checkpoints AFTER file edits instead of before
- Add checkpoint before processing new user prompts
- Fixes regression where checkpoints were only saved before file edits

Fixes #6800

Author: roomote

src/core/assistant-message/presentAssistantMessage.ts

@@ -410,8 +410,9 @@ export async function presentAssistantMessage(cline: Task) {
 
 			switch (block.name) {
 				case "write_to_file":
-					await checkpointSaveAndMark(cline)
 					await writeToFileTool(cline, block, askApproval, handleError, pushToolResult, removeClosingTag)
+					// Save checkpoint AFTER file edit
+					await checkpointSaveAndMark(cline)
 					break
 				case "update_todo_list":
 					await updateTodoListTool(cline, block, askApproval, handleError, pushToolResult, removeClosingTag)
@@ -430,10 +431,8 @@ export async function presentAssistantMessage(cline: Task) {
 					}
 
 					if (isMultiFileApplyDiffEnabled) {
-						await checkpointSaveAndMark(cline)
 						await applyDiffTool(cline, block, askApproval, handleError, pushToolResult, removeClosingTag)
 					} else {
-						await checkpointSaveAndMark(cline)
 						await applyDiffToolLegacy(
 							cline,
 							block,
@@ -443,15 +442,19 @@ export async function presentAssistantMessage(cline: Task) {
 							removeClosingTag,
 						)
 					}
+					// Save checkpoint AFTER file edit
+					await checkpointSaveAndMark(cline)
 					break
 				}
 				case "insert_content":
-					await checkpointSaveAndMark(cline)
 					await insertContentTool(cline, block, askApproval, handleError, pushToolResult, removeClosingTag)
+					// Save checkpoint AFTER file edit
+					await checkpointSaveAndMark(cline)
 					break
 				case "search_and_replace":
-					await checkpointSaveAndMark(cline)
 					await searchAndReplaceTool(cline, block, askApproval, handleError, pushToolResult, removeClosingTag)
+					// Save checkpoint AFTER file edit
+					await checkpointSaveAndMark(cline)
 					break
 				case "read_file":
 					await readFileTool(cline, block, askApproval, handleError, pushToolResult, removeClosingTag)