Let me direct you to (and I'm by far not trying to pat myself on the back here, but I searched long and hard to come up with what I have, so consider it a smorgesboard (sp?) of my experiences with these same questions)
cksec, in particular check out the verifyfile() sub (must carefully read all of the sub) which makes sure a file is what it should be. Also, check out the updatedb() sub, which actually writes to a file and so ensures that it is what it should be.
I wish I could remember where I found this info, in order to give credit to the author, unfortunately I cannot...wait...ah yes, it's from the book
Perl for Systems Administrators, which while having too much Windows stuff for my taste, has some great info.
Hope I've helped, enjoy!
