Hi Andrew and others,
I spent a lot of time a few months ago working on $subj. After many dead
ends, I decided it was more prudent to spend my time working on other
issues. I have now returned to this issue and would like to pass it off to
those who will have more luck than I did figuring out what is going wrong.
RH Bug #161483 
CVS checkouts in Eclipse take an extremely long time to finish when run
under gij. The issue occurs both when the relevant jars are
natively-compiled and when they are not (although the problem is
exacerbated when run with only bytecode). I have found a few modules that
replicate the issue but the one I have used the most is GNU Classpath. The
problem is independent of network issues as checkouts from a local CVS
server exhibit the same behaviour.
Things to note:
The problem appears to be related to some sort of thread contention. I
wrote a headless Eclipse CVS client (using the same code as the GUI CVS
client) that does not reproduce the problem. Following the actual checkout
of the files from CVS, Eclipse creates synchronization information for the
files it has just checked out. Since this is an initial checkout, all
folders are considered dirty so it descends into each folder. One of my
original theories was that we were incorrectly computing dirty resources
(or getting into some sort of recursive loop) but this is not the case.
Much println'ing has told me that both gcj and the Sun JVM come up with the
same list of dirty folders.
Timing information that I have accumulated has shown that we are not
spending an inordinate amount of time generating or writing the
synchronization information but are instead spending too much time holding
locks on the resources. On average we are holding the locks about 100 -
1000 times longer than the Sun JVM. This can be verified by a sysprof 
sample  taken which shows a lot of time in Semaphore.acquire().
OProfile results corroborate this evidence.
gnuplot was used at one point to see if the time spent was proportional to
the number of files in the directory or to the disk space of said files.
No correlation was observed.
Note: at one point, I thought the problem was due to missing .sos for some
jars because I could not duplicate the problem on my laptop. It turns out
that if I changed the CVS compression level , I could somehow affect the
timing such that it would indeed occur. Hyperthreaded machines seems
impervious to this.
There appears to be no way to reduce this to a test case so we are
unfortunately left with duplicating the symptoms using Eclipse itself.
How to duplicate:
I have created a version of Anthony's excellent redhat-eclipse-demo RPM
that contains a snapshot of GNU Classpath (from a while ago). This RPM
will create a local pserver CVS server running on port 2402. It will also
create the user anoncvs and put an exploded GNU Classpath checkout (owned
by this user) in /var/lib/eclipse-demo-cvsroot. You can retrieve a copy of
this RPM here:
1. Install Eclipse from either FC4 or rawhide. gcc versions do not seem to
affect this problem and I've done most of my testing with 4.0.2-3 which was
current in rawhide until recently.
2. Fire up Eclipse with a new workspace ... something like:
eclipse -data ~/testcvsissueworkspace
3. Checkout classpath from your local CVS server:
File->Import->Checkout Projects from CVS
pserver, 2402, check 'Save password'
4. Observe that checkout hangs at final synchronization
I am at a bit of a loss as to how to proceed. Any and all help is greatly
appreciated. I will provide whatever information is necessary. (I wrote
this email while on a plane and lost a bit of revision I had done just
before my battery died. If anything's amiss, I blame that ;)