The plugin folder should be outside the Mac bundle so that it is not overwritten every time the bundle is updated.
Implemented in SVN (/trunk).
The plugins are now read from the installation folder first, then from <home>/plugins, <home> being the user preference location as defined in the documentation.
Note that no attempt is made to check whether a plugin is loaded twice, so the same plugin shouldn't be both in the installation folder and in <home>/plugins. If that happens, unexpected behaviour can occur.
This feature was implemented in the released version 2.5.2 of OmegaT.