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I was running a happy 4.2 Eclipse (RCP package) and did a Check for Updates that pushed me over to 4.2.1 and now Help/Install new software has NO available software sites defined!
Moving to the EPP package.
FWIW, one of Zend Studio users hit the same issue: http://forums.zend.com/viewtopic.php?f=59&t=127038 Both version 12.5 and 12.5.1 of Zend Studio are based on Eclipse 4.4.2. I hear for such issue for first time, I am not able to reproduce it, so it seems to be some rare issue. And definitely not one related to the EPP packages, but to the Platform itself.
I think this bug report should be closed as duplicate of Bug 502524. The other one has been created later, but it showed at least some activity in 2019.