I checked out some files from an svn repo.

Renamed a file. Say changed X.php to Y.php.
Then I created a new X.php from the filesystem outside of Netbeans.
The file X.php in the file list showed up grey with status saying Locally Deleted. 
This leaves no way to sanely commit the file as an update.

To work around I had to update the directory and get the original file from the repository then I copy pasted the
complete new file into the new file and saved the new file. This makes it a bit awkward to do this type of thing.

I vaguely remember that IDEA was able to figure out that a file was really changed not deleted in this situation.
Something like that is needed.