Every change in your directory structure is reported when running Eyesite.
After a change this is reported as long as you did not accept it. You can have an email when Eyesite discovers a change. You can include and exclude directories, list file extensions to monitor and exclude files from monitoring.
The only thing I must remember is to see and accept all the changes after an update of Joomla or extensions.
Using a (paid) plugin helps to scan your maps on a regular base (every X hour) automated.
I found some issues, which were solved very fast (big support).
As a reward i did send the dutch translation.
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But I must say the performance has speeded up, more than the developer claims. I measured a 20% improvement in the latest release.
But it is as he says "may vary per server/setup"
I am sorry. The new version should reduce that speed improvement to 0% again.