2) Allow the user to provide CLI commands to customise the server

This is by far my favorite approach. The provisioning file would just 
contain a list of CLI commands, and would execute them in order. I think 
this is by far the most intuitive, and the CLI is well documented.

3) Allow the user to provide DMR operations to customize the server

Similar to 2, but allow the user to provide DMR or JSON operations to 
customize the server. I think this is not nearly as nice as 2, as users 
are much more likely to be familiar with the CLI rather than DMR.