Comment 1 for bug 946865

If you want a hand-crafted zope.conf, use the zope-conf option of the p.r.zope2instance recipe and point to a location outside parts or if possible do them via the zope-conf-additional option, so they'll get regenerated on each buildout run.

If you depend on extensions, better put them inside a product and keep them out of the instance home. Any package using the "Products" namespace can contain an extensions folder, see for example https://github.com/plone/Products.CMFQuickInstallerTool/tree/1.6/Products/CMFQuickInstallerTool/Extensions.

It's part of buildouts design to wipe anything in the parts folder at pretty much any moment. Anything that's inside parts needs to be recreated by the responsible recipe on each run. For zope.conf there's two options that cover this already. Extensions are such an outdated concept, that I wouldn't want to do anything to encourage their use or document them any further.