fix: clear all marks not persisting changes (#17)

The UI was calling storage.clear_all_marks() directly which only cleared
marks in memory. Now uses the main module's method to properly save changes.

Solves: #16

Author: alexekdahl

lua/marksman/ui.lua

@@ -438,8 +438,8 @@ local function setup_window_keymaps(buf, marks, project_name, mark_info, search_
 			prompt = "Clear all marks in this project?",
 		}, function(choice)
 			if choice == "Yes" then
-				local storage = require("marksman.storage")
-				storage.clear_all_marks()
+				local marksman = require("marksman")
+				marksman.clear_all_marks()
 				close_window()
 				notify("󰃀 All marks cleared", vim.log.levels.INFO)
 			end

tests/marksman_spec.lua

@@ -155,6 +155,45 @@ describe("marksman.nvim", function()
 			result = marksman.delete_mark("nonexistent")
 			assert.is_false(result.success)
 		end)
+
+		-- Test case for the clear all marks bug fix
+		-- This ensures that clearing all marks through the UI properly persists the changes
+		it("clears all marks and persists changes", function()
+			vim.cmd("edit " .. test_file)
+
+			-- Add multiple marks at different positions
+			marksman.add_mark("mark1")
+			vim.fn.cursor(2, 1)
+			marksman.add_mark("mark2")
+			vim.fn.cursor(3, 1)
+			marksman.add_mark("mark3")
+
+			-- Verify marks were added
+			assert.equals(3, marksman.get_marks_count())
+
+			-- Mock vim.ui.select to automatically confirm the clear action
+			local original_select = vim.ui.select
+			vim.ui.select = function(choices, opts, callback)
+				if opts.prompt == "Clear all marks in this project?" then
+					callback("Yes") -- Simulate user selecting "Yes"
+				end
+			end
+
+			-- Clear all marks (this should trigger the save mechanism)
+			marksman.clear_all_marks()
+
+			-- Restore original function
+			vim.ui.select = original_select
+
+			-- Verify marks were cleared immediately
+			assert.equals(0, marksman.get_marks_count())
+
+			-- Wait for any debounced save operations to complete
+			vim.wait(200)
+
+			-- Verify marks remain cleared after save delay
+			assert.equals(0, marksman.get_marks_count(), "Marks should remain cleared after debounced save")
+		end)
 	end)
 
 	describe("mark search and filtering", function()