Enhance git metadata handling and improve change detection logic

- Introduced a new function `getGitMetadata` in `ApiContext` to fetch current git metadata, including new file IDs.
- Updated the `PatchTree.build` function to handle new file IDs, allowing for better differentiation between tracked and untracked files during patch processing.
- Modified the `git_changed_files` function to return both tracked and untracked files, improving accuracy in change detection.
- Enhanced the `App` component to debounce git metadata refreshes, ensuring the UI reflects the latest changes without unnecessary calls.

These changes aim to improve the integration with git and enhance the accuracy of change detection in the application.

plugin/src/App/init.lua

@@ -1000,6 +1000,9 @@ function App:startSession()
 		return result
 	end)
 
+	local pendingGitRefreshThread = nil
+	local GIT_METADATA_DEBOUNCE = 0.5
+
 	serveSession:setPatchUpdateCallback(function(instanceMap, patch, changedIds)
 		-- If all changes have been reverted, auto-accept the empty patch
 		if PatchSet.isEmpty(patch) then
@@ -1009,14 +1012,40 @@ function App:startSession()
 			return
 		end
 
-		-- Update the patchTree when new changes arrive during confirmation
-		-- The changedIds parameter contains IDs of items that were modified
-		-- so their selections can be reset (user must re-review)
+		-- Immediately rebuild with stale metadata so the UI reflects new items
 		local gitMetadata = cachedServerInfo and cachedServerInfo.gitMetadata
 		self:setState({
 			patchTree = PatchTree.build(patch, instanceMap, { "Property", "Current", "Incoming" }, gitMetadata),
-			changedIds = changedIds, -- Pass to UI so it can unselect changed items
+			changedIds = changedIds,
 		})
+
+		-- Debounce: schedule a fresh git metadata fetch after rapid patches settle
+		if pendingGitRefreshThread then
+			task.cancel(pendingGitRefreshThread)
+		end
+		pendingGitRefreshThread = task.delay(GIT_METADATA_DEBOUNCE, function()
+			pendingGitRefreshThread = nil
+			apiContext
+				:getGitMetadata()
+				:andThen(function(freshMetadata)
+					if cachedServerInfo then
+						cachedServerInfo.gitMetadata = freshMetadata
+					end
+					if self.state.appStatus == AppStatus.Confirming then
+						self:setState({
+							patchTree = PatchTree.build(
+								patch,
+								instanceMap,
+								{ "Property", "Current", "Incoming" },
+								freshMetadata
+							),
+						})
+					end
+				end)
+				:catch(function(err)
+					Log.warn("Failed to refresh git metadata: {}", tostring(err))
+				end)
+		end)
 	end)
 
 	-- One-shot sync: disconnect after initial sync is fully complete (including any writes)