I ran into this issue this week. My special wrinkle: I have JULIA_PKGDIR set to point to a non-default location (a network share, in fact). Deleting the lib/v0.6 directories in both the usual place and under the directory specifed by JULIA_PKGDIR and restarting was insufficient to fix things for me. The extra tweak I made that got things to work was to prepend the <my_pkgdir>/lib/v0.6 path to Base.LOAD_CACHE_PATH and then rebuild the failing packages.