Initialize should not be destructive on main drive

[joepio]

@AlexMikhalev had an issue where after running --initialize:

• Run atomic server
• Set some rights on your main drive (e.g. invite your existing agent)
• Run again with --initialize
• Rights are removed / reset

I think this can be fixed by making --initialize additive instead of destructive.

[Polleps]

Ideally you shouldn't need to run --initialize again at all. Wouldn't it be better to either fix the issues that require you to rerun this or to give other options like --reset-admin-agent and/or --rebuild-default-resources