Que tal algo simples como calcular o md5sum para cada arquivo e classificar com base no hash.
md5deep -r . | sort
d921223ccbe759a632973962bc15a497 /root/.bash_history
dcac40478a92e87cd08a42a6425acea6 /root/testsrv/keys/04.pem
dcac40478a92e87cd08a42a6425acea6 /root/testsrv/keys/client2.crt
e12f5739f81b08c470f20890304bf53e /root/.bashrc
e1b23db3d2293b142938c74649d9fa6a /root/testsrv/list-crl
e4e2818e1ed11a951ed5da4e1a86885a /root/testsrv/keys/revoke-test.pem
ee8bd2ea88220c877a62e22e36a02d20 /root/testsrv/keys/index.txt.attr
ee8bd2ea88220c877a62e22e36a02d20 /root/testsrv/keys/index.txt.attr.old