Oh, yea, I agree. WinMerge is a bit of a hack. Kind of the nature of the beast when running with continual builds.
As for development, I think the hot tip would be to basically create your own domain (asadmin will do this for you), but DO NOT place the domain in the GF tree (i.e. under $glassfish/domains).
Rather, just put it someplace completely different (/usr/local/domains maybe, or ~/domains).
The domain dirs are REASONABLY "standalone".
The GF install is quite position dependent (well, asenv.conf is, but anyway), but the domains can be anywhere.
You may very well have good success with simply upgrading your server (or installing in a new place) and then having it start your existing domain.
i.e. upgrade the server, but don't upgrade the domain.
The primary reason to upgrade the domain is if you're after some of the fancier GF things (like the JBI stuff, etc.). Because those are really just applications installed in the domain (at least at the moment).
But most of Glassfish is NOT in the domain, it's in the root install.
So, while not guaranteed (especially if you're using the JBI stuff), odds are really high that you'll be able to upgrade your server WITHOUT touching your domain. Obiviously, they're free to tweak the DTDs and stuff, but now that they've hit RC1 for v2, that's REALLY unlikely going forward.
The biggest downside is you may not automatically get some new feature (because your old domain doesn't have it "installed"), but you should get all of the bug fixes and such for your current domain using the features you're app is already using.
But, again, now that they've hit RC1, probably not a real concern going forward until you start playing with GFv3 (then the wheel goes round and round again...).
And, of course, if there are problems you'll likely find out instantly when you start the server as it whines and moans about an ugly domain.xml file.
Hopefully the GF team can comment on this stragety.
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