1. Обсуждение нужной вам функции
youtrack.jetbrains.net/issue/WI-717
2. Голосование за нее
youtrack.jetbrains.net/issue/WI-343
3. Решение из первого пункта по удалению каталога из контроля версий:
So if you want SVN to ignore it you should remove it from version control.
1) close phpstorm
2) make a backup of .idea folder
3) make svn delete .idea folder
4) commit deletion — svn should delete this folder locally now
5) restore original .idea folder at its place
6) make sure there is no .svn folder in .idea folder
After that according to your screenshot3.png you should have no problems with .idea folder.