Restoring the Default Set of Mac Fonts
fontrestore (via Charles Edge):
fontrestore detects fonts in /Library/Fonts, /System/Library/Fonts, and ~/Library/Fonts which are not part of the system install and moves them to /Library/Fonts (Removed), /System/Library/Fonts (Removed), and ~/Library/Fonts/Fonts (Removed) directories. Critical fonts required for operation of the user interface are also restored.
I guess this is the terminal equivalent for Font Book > File > Restore Standard Fonts...?