Improve current documentation around keys and certificates

[brantgurga]

The existing Security.MD mentions including a keystore but fails to mention sequencing it after any feature.sh and configure.sh call since those overwrite the keystore.
The Security.MD also doesn't mention the container startup will fail if the key file used is encrypted since no method is provided to decrypt it.

[brantgurga]

Pull request #514 is proposed as a way to improve the documentation.