You'll have to violate the iso9660 standards but it is necessary if you want to preserve your filesystem and filenames and shouldn't be an issue as long as you are using a modern OS like Linux.

genisoimage -o Backup-Myfiles.iso -r -J -joliet-long  /some/path/

You will get errors like below (even enabling joliet-long didn't help)

genisoimage: Error: /some/filename.pdf have the same Joliet name
Joliet tree sort failed. The -joliet-long switch may help you.

#the best way

genisoimage -o /tmp/Backup-Myfiles2.iso -U -iso-level 4 -R  /source/dir

This was the only way I could get unmodified long file names and VERY deep directories onto the iso image as original otherwise they get renamed and truncated which breaks a lot of things and makes it confusing.  But be warned this breaks the iso9660 standard so many OS's especially Windows may not be able to read it.

==========

#this fixes it
-R is for Rock Ridge and allows for more than 8 deep folders
-U allows for untranslated filenames

genisoimage -o /tmp/Backup-Myfiles.iso -R -U  .

#with an exclude

genisoimage -o /tmp/Backup-Myfiles.iso -R -U -m WebSites/blabla .
Warning: creating filesystem that does not conform to ISO-9660.
I: -input-charset not specified, using utf-8 (detected in locale settings)


#the -m causes a shrink error unless you put it earlier


genisoimage: File 'blank.html' did shrink.
Files must not be changed while genisoimage runs!

genisoimage -m WebSites/blabla -o /tmp/Backup-Myfiles.iso -R -U  .

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