[Plugin: WordPress File Monitor] legitimate modifications vs non

Hello! I have been installing this plugin on my customer’s sites, thinking it would be incredibly helpful, but now my concern is that I am going to be inundated with daily email messages with each of them sending me their WP File Monitor daily log files, asking me if all of the entries are “ok” (i.e., something they did) vs a hacker’s attempt. Most of these sites are active sites. That is, the owner blogs a lot, or has a membership site where they teach online and students post on various pages of the site. If the sites were rather static, then I’d say any notification of a file change might be suspicious. How on earth do I weed through what folders could be safely exluded from the monitoring, vs which ones we need to keep an eye on, and who has time or the knowledge to look at hundreds of files listed on a daily report? For example, today I installed a plugin on a site and we made a few changes, and the list of files changed and deleted was hundreds of lines long. Thanks for ANY advice!!

http://wordpress.org/extend/plugins/wordpress-file-monitor/