How can I remove duplicate files across separate directory trees?
Solution 1:
Of course! Check out FSlint:
FSlint is a utility to find and clean various forms of lint on a filesystem. I.E. unwanted or problematic cruft in your files or file names. For example, one form of lint it finds is duplicate files. It has both GUI and command line modes.
FSlint is free and open source software.
Solution 2:
fdupes - finds duplicate files in a given set of directories
fdupes new/ old/
-d for delete
-N for don't ask
fdupes -N -d new/ old/