Experimente a opção -l
. De man md5deep
:
-l Enables relative file paths. Instead of printing the absolute
path for each file, displays the relative file path as indicated
on the command line. This flag may not be used in conjunction
with the -b flag.
Então faça:
cd /home/user/
md5deep -lrs Documents > checksum.md5
Por exemplo,
$ md5deep -lrs Downloads | head -1
699cd26d7fe0bada29eb1b2cd7b50e4b Downloads/Sublime Text 2.0.2 x64.tar.bz2