Browser specific code: All browser-specific code lies under a directory with the browser's name. For example: JS code specific to the Chrome extension lies inside: Chrome/glee_chrome/js/chrome/. And JS code specific to Safari lies inside Safari/gleeBox.safariextension/js/safari/. Everything else is the core gleeBox code.

Making changes to core gleeBox code: If you're coding a new feature or fixing a bug in the core gleeBox code, make the changes in the Chrome extension: Chrome/gleebox_chrome first.
Then, to apply these changes in Safari, run Safari/update.sh. Important: Right now, you need to run update.sh from Safari/.

There is one exception to the second rule above. Any changes made to options.html in Chrome are not copied to Safari on running update.sh. You'll need to do those manually. This is because Safari's option.html is slightly different from Chrome's options.html (does not have options for Sync and Bookmark Search).

Currently, Firefox and UserScript versions are very outdated. You may not make any changes to them. The plan is to start fresh for both of them.