If what you want is a file integrity checker, then RPM will do what you want. `rpm -qaV`(note the uppercase V). That will go through and check:
* file size
* mode(permission and file type)
* MD5 checksum
* device number(checks if someone's hiding a file by mounting another partition there
* readlink path(if the symlink points to a different file)
* user ownership
* group ownership
* modification time
That should be a fairly comprehensive list.
`rpm -qa --filesbypkg | awk '{print $2}'` will list all the files on the system that have been accounted for.
`find / | grep -vf /tmp/files-on-system.txt` will find all files on the system that are not in the RPM database. Another way of accomplishing these two commands in one command would be `rpm -qf 'find /'#replace single quote with backtick` **NOTE: This will also flag as erroneous files in directories like
* `/dev`
* `/home`
* `/proc`
* `/var/run`
* `/var/log`
* `/var/lib`
* `/tmp`**