Fix: Path handling in project files

Because of cleanPath() converts native separators to '/',
call toNativeSeparators() after cleanPath().

Due to warning message from "if (exists(filePath))" on Windows,
if() around the exists() are removed.

Change-Id: I412fe83f13365c8eec00e119270d07ce7f72297d
Reviewed-by: Oswald Buddenhagen <oswald.buddenhagen@digia.com>