Add: preserve undo history using neotree toggle while closing a buffer

lua/keymaps.lua

@@ -209,11 +209,7 @@ local function smart_save(force_save_as)
 			return
 		end
 	end
-	-- Preserve cursor position and undo history
-	local cursor_pos = vim.api.nvim_win_get_cursor(0)
 	vim.api.nvim_buf_set_option(0, 'modified', false)
-	vim.api.nvim_win_set_cursor(0, cursor_pos)
-
 	print('Saved ' .. filename)
 end
 -- Save current buffer
@@ -268,8 +264,30 @@ local function is_alpha_running()
 	end
 	return false
 end
+-- Helper function: toggle Undotree to preserve undo history for root-protected files
+local function toggle_undotree_twice(callback)
+	local filename = vim.api.nvim_buf_get_name(0)
+	if filename ~= '' and vim.fn.filereadable(filename) == 1 and vim.fn.filewritable(filename) == 0 then
+		if vim.fn.exists ':UndotreeToggle' == 2 then
+			vim.cmd 'UndotreeToggle'
+			vim.defer_fn(function()
+				vim.cmd 'UndotreeToggle'
+				if callback then
+					vim.defer_fn(callback, 50)
+				end
+			end, 50)
+		elseif callback then
+			callback()
+		end
+	else
+		if callback then
+			callback()
+		end
+	end
+end
 -- Main function
 local function close_window(mode)
+	local function do_close()
 		local bufnr = vim.api.nvim_get_current_buf()
 		local modified = vim.bo.modified
 		local buftype = vim.api.nvim_buf_get_option(bufnr, 'buftype') -- detect terminal buffer
@@ -351,6 +369,9 @@ local function close_window(mode)
 				vim.cmd 'bdelete'
 			end
 		end
+	end
+	-- Toggle Undotree before closing to ensure undo history is preserved
+	toggle_undotree_twice(do_close)
 end
 -- Asks what to do if the window is unsaved, otherwise just close
 vim.keymap.set('n', '<leader>q', function()