tests(cmd): clean and prepare the prefix directory for each test case

This ensures that the prefix directory is reset to a known state after
other test runs (and in between individual test cases), fixing a
flakiness issue we've been seeing in CI:

> FAIL spec/02-integration/02-cmd/06-restart_spec.lua:23: kong restart restarts if not running
> spec/02-integration/02-cmd/06-restart_spec.lua:26: Error: in-memory storage can not be used when role = "control_plane"
>
>  Run with --v (verbose) or --vv (debug) for more details

spec/02-integration/02-cmd/06-restart_spec.lua

@@ -7,11 +7,14 @@ end
 describe("kong restart", function()
   lazy_setup(function()
     helpers.get_db_utils(nil, {}) -- runs migrations
-    helpers.prepare_prefix()
   end)
   lazy_teardown(function()
     helpers.clean_prefix()
   end)
+  before_each(function()
+    helpers.clean_prefix()
+    helpers.prepare_prefix()
+  end)
   after_each(function()
     helpers.kill_all()
   end)