David,
I understand the frustration that this issue causes, but you’re directing your ire at the wrong support group. As you mentioned, this problem is a “show stopper” bug in the Eclipse M4 codebase, not in ours. Here’s the support forum topic that you started previously that runs it down.
https://www.genuitec.com/forums/topic/cannot-open-java-source-file-closed/
The workaround is to use 2.1.1/2.1.2 and MyEclipse 2.6.4 if you must use external links. The functionality in the two MyEclipse versions is identical and problems like the M4 links bug is why we strongly recommend that everyone use 2.1.x for all production work. The Eclipse M-builds are simply not stable enough for production use, in our opinion. On the plus side, the Eclipse team fixes bugs like this rapidly so it should be addressed in the M5 release, which is only a few weeks away. Please hang in there with the workaround in the meantime. 🙂
–Scott
MyEclipse Support