Have you got the "already under version control" error message when commiting or trying to add to a repo from aptana? I found it was because I had copied folders from another part of my project that was already in SVN. It also copied the .svn folders so Aptana thought it was already in the SVN.
The fix is to delete the .svn folders (don't forget they can also be in the sub folders).
find ./ -name ".svn" | xargs rm -Rf
Source: http://cephas.net/blog/2007/04/06/command-line-script-to-delete-svn-files-folders/