Using jedit trunk with the Mac OS X plugin (SVN revision 23203), the Apple Preferences menu item uses the official Apple key for that: COMMAND comma. This is in conflict with the traditional jEdit shortcut quick-search.shortcut=C+COMMA.
Even in keymaps/Mac_OS_X_keys.props there is no attempt yet, to evade to a different key. Alternatively, one could try to convince the Apple application wrapper not to use their standard key, but hardcore Mac users might complain.
Committed rev 23207 to the mac keymaps file.
Do we need to change the default jEdit keymap? Personally, I don't even look at it anymore since I am maintaining the emacs keymap.
If you think there are other changes that are needed to the mac os x keymap, you can commit those directly.
oops. my fix introduced another conflict. I don't know what the appropriate key is. Can you fix this yourself?