Diffing two filesystems
Solution 1:
Use rsync with --dry-run option.
For monitoring local changes, use tripwire.
Solution 2:
There is a tool called fsdiff [I could not find the homepage] that will compare a filesystem to its transcript. A free, multi-platform tool called radmind includes it and claims,
At its core, radmind operates as a tripwire. It is able to detect changes to any managed filesystem object, e.g. files, directories, links, etc. However, radmind goes further than just integrity checking: once a change is detected, radmind can optionally reverse the change.