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One thing that "regressed" in fixing bug 404593 was that some of the code that uses the "common" version of base builder assumed the 'eclipse executables' had already had 'chmod' applied to make them executable. Emphasizes need to use a common script to "get and prepare" basebuilder. Current thought is to move 'getBaseBuilder.xml' to more common location (under tychoeclipsebuilder) and invoke it with ant, when ever needed. It is a bit over engineered for current needs (e.g. can get base builder from cvs or git) but having a "common script" will make it easier to move off of base builder and use Eclipse Platform instead (with suitably p2 installed tools and apps).
We have stopped using "basebuilder" but did not solve it exactly this way.