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...you shouldn't need to do it yourself (and it's involved, you have to build your own make file essentially, compile w/java, etc. etc.)
8.5.0 should automatically flatten your JS files, but not CSS. I think in 8.5.2 they're trying to flatten the CSS as well but I'm not sure.
Search this forum for my name and "custom build", you should find a couple of discussions on this topic. I would open a PMR with Lotus Support about it too so you can be added the SPR. They might have more information about it to share with you also.
Feedback response number ECBS86HPGS created by ~Dana Elfreekony on 06/17/2010