For files and directories, use a version control system. I'd use git, for which CPAN modules are available. You can check the cleanness of an entire repository with a single command. For a database, I'd probably record and verify transaction IDs.

perl -le'print map{pack c,($-++?1:13)+ord}split//,ESEL'

In reply to Re^3: Method to verify an environment with changes by shmem
in thread Method to verify an environment with changes by gtk

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