I had been holding off on upgrading to Mavericks for fear that it would break thinks and it seems my fears came true. I had a stock Homebrew install with lots of compiled tools linked to /usr/local/bin and some custom links to other binaries, for example a shortcut for Sublime Text. After upgrading to Mavericks, the folder was cleared of almost everything, and therefore none of the commands work. The brew script remained, and some latex tools but that appears to be it.
Is this an expected behavior upon the upgrade and is there any quick fix for it? Can I just copy the folder contents from a backup?
I just noticed that /usr/local/lib seems to have suffered a similar fate, if that matters to any answers. I'm worried what else might have been affected. Has anyone else experienced this behavior?