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Do you know of any linux program, that would monitor accesses to directories and files in the filesystem? I would like to able to produce some report of how many times certain files were accessed in some period?
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You probably want inotify-tools. Inotify is part of the linux kernal that triggers events on watched files, directories, or even the contents of entire directories. These tools are command line utilities that tap into the capabilities of inotify and allow you to use them, for example, in your shell scripts.
Specifically, you will probably want to look at
inotifywatchMaybe that's what you need: http://www.cyberciti.biz/tips/record-monitor-linux-filesystem-changes-auditing.html