I have a folder where I keep checked-out version from Aptana Subversive SVN plugin. I have another folder where the checked-out copy from Eclipse resides. Both, Aptana & Eclipse, are using the same repository. Though the repository is the same, but I am using two different working folders. Sometimes I use Eclipse to work with the same set of files in the repository and sometimes I use Aptana.
I want a tool that can synchronize the two working folders automatically. Is there any free tool?
Actually, SVN is the tool to do just that. If you fight SVN, you will run into trouble, because you might not have both working copies updated to the same the same revision, the merge tool messes up the hidden .svn folders and whatnot.
Why do you think you need to manually synchronize those two working copies? If you want to work on both simultaneously without disrupting other's work because you keep checking in half-baked things, consider working on a branch. Doing so, you make use of SVN, which was designed to keep two working copies in sync. If you're done with whatever you're doing, merge that branch into the trunk (or whatever branch you were working at) and throw it away.
If you feel like all this checking in might make your repository become too big, get a bigger disk to store it on. The very first time you or that tool messes up manual merging, it would have payed off. If you're afraid of bumping SVN's revision count without doing actual work, get a grip.