I do this with Git. Simply, create a Git repository of your directory:
git-init
git add .
git commit -m "Done"
Insert the stick, cd to directory on it (I have a big ext2 file I mount with -o loop), and do:
git-clone --bare /path/to/my/dir
Then, I take the stick to other computer (home, etc.). I can work directly on stick, or clone once again. Go to some dir on the hard disk and:
git-clone /path/to/stick/repos
When I'm done with changes, I do 'git push' back to stick, and when I'm back at work, I 'git push' once again to move the changes from stick to work computer. Once you set this up, you can use 'git pull' to fetch the changes only (you don't need to clone anymore, just the first time) and 'git push' to push the changes the other way.
The beauty of this is that you can see all the changes with 'git log' and even keep some unrelated work in sync when it changes at both places in the meantime.
If you don't like the command line, you can use graphical tools like gitk and git-gui.
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