Does TheIDE handle upgrades at all?
Basically under Linux, the library files are copied to each user's home directory (at least thats whats recommended). So if the admin wanted to update the files, it looks like he would have to manually replace the main install files as well as all the files in all the users' directories.
A "simple fix" might be to have TheIDE Linux store a file with the user's local library version. Upon opening, it compares that to the main install's version file. If main>local, popup a dialog asking if you want to upgrade local files.
(this is looking forward to package-managed installs)
Think about it - they are not necessarily stored in home. That is just the simplest setting. Even linux readme offers the possibility to place them into usr/local.
However, note that all this is just for initial setup when a couple of standard assemblies is created. You can make your own assemblies and place uppsrc anywhere you want.