I installed FC5 on my machine.
First I backed up $HOME, then I did a clean install.
Then I copied $HOME back.  Then I ran Eclipse.

Eclipse forgot about my local update site in ~/.eclipse/.
So, it couldn't find the pllugins I had installed.
However, the behavior was a bit odd... I went to the 
eclipse.org update site, but Eclipse didn't offer me any
updates -- as if it still partially knew about some of
my local installs (like GEF).

I manually added ~/.eclipse/.../whatever as a local site
and restarted, and then all was fine.  However it would be
preferable not to have to go through this with updates.