Removing develop-eggs/ directory before bootstrapping.
There is code in buildout to remove develop-eggs that it knows about. So if everything is OK, develop-egg removal works fine. If there's something fishy goign on, however, buildout doesn't clean it up enough. Zapping the entire directory upon bootstrap is a very effective way to prevent problems. Reason: the old osc.recipe.sysegg did add develop-eggs .egg-link files to the site-packages dir, effectively short-circuiting buildout's picked versions. Likewise an old bootstrap could have left a setuptoos.egg-link to an ancient setuptools version. I just this minute had to help a colleague with just such a problem.
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