to learn a bit about vocabulary. IIRC Dry Lavigne in 100 BSD hacks have described use of mtree to built a primitive HIDS. Building a real HIDS would require some serious knowledge of machine learning (anomaly detection).
My personal favorite to check for rootkits is security/rkhunter, fully integrated with FreeBSD and supports a large variety of rootkit checksums.
When it comes to checking for changed files (note that rkhunter can also do that to a certain degree) then you'd want an IDS (Intrusion Detection System). There are plenty, as Oko mentioned there's even mtree which is provided in the base system. However, I've become a big fan of security/tripwire. A full blown IDS which can check for just about everything. I've posted a tutorial on setting up & using Tripwire, maybe it can give you some impressions. You can find that tutorial here.
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