I moved to a new machine, and Migration Assistant failed miserably. I had to move files by hand, and in doing so some mighty strange things started happening.
I have finally tracked these down. Many of the files on both of the drives on this machine have a "Everyone: Custom" setting as the first permission. In this Custom setting, I don't have read/write, only read, and that means I can't (for instance) write to my own ~/Library
Disk Util was run, and resetpassword, and these each fixed some of the problems. I can edit most files, build in Xcode, etc.
But this did NOT fix my Library, so I can't (for instance) write to my keychain.
So... any suggestions on how to fix this? I know I want to remove all these Custom's, but perhaps there's some files in there that need them? Or should I simply chown everything in there and change the permissions to me read/write?