After many calls with the Apple support, they told me I should reinstall the OS and restore my stuff with the migration assistant. I did it and almost everything works fine so far.
Only brew doctor
shows me a few errors. I could fix the most of them by myself. I just don't know the most elegant way to solve the following error:
localhost:~ Newton1$ brew doctor
Warning: Broken symlinks were found. Remove them with "brew prune":
/usr/local/share/ghostscript/9.07/Resource/Font/xylubt12.pfb
/usr/local/share/ghostscript/9.07/Resource/Font/xylubt11.pfb
/usr/local/share/ghostscript/9.07/Resource/Font/xylubt10.pfb
/usr/local/share/ghostscript/9.07/Resource/Font/xyluat12.pfb
/usr/local/share/ghostscript/9.07/Resource/Font/xyluat11.pfb
/usr/local/share/ghostscript/9.07/Resource/Font/xyluat10.pfb
.
.
.
/usr/local/share/ghostscript/9.07/Resource/Font/blex.pfb
/usr/local/share/emacs/site-lisp/subdirs.el
/usr/local/share/emacs/site-lisp/autotest-mode.elc
/usr/local/share/emacs/site-lisp/autotest-mode.el
/usr/local/share/emacs/site-lisp/autoconf-mode.elc
/usr/local/share/emacs/site-lisp/autoconf-mode.el
/usr/local/share/emacs/24.3
/usr/local/share/applications/emacs.desktop
/usr/local/Frameworks/Python.framework/Versions/Current
/usr/local/Frameworks/Python.framework/Versions/2.7
/usr/local/Frameworks/Python.framework/Resources
/usr/local/Frameworks/Python.framework/Python
/usr/local/Frameworks/Python.framework/Headers
I think now you know what I mean. And there are much more entries.
So, how I can fix it as easily as possible?