Compare them without the ELF headers, a section at a time, so
that the timestamps are irrelevent.

You may also have to throw out the "what" information from the
binaries, preemptively...

Julian Elischer wrote:
> 
> I have two directories of executables
> (actually two entire FreeBSD filesystems)
> 
> they were both produced from the same checked out trees except that
> between the two compiles, some patches (unknown) were applied
> to the sources.
> 
> How can I find out which binaries have changed?
> they are all different according to cksum so I assume
> that there is a timestamp or something in them.
> Is there a way to compare only the text segments?
> 
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