Don't create CA-only dirs with init-pki command

These directories are only created when building a CA, and subsequently
checked for only when performing CA-specific tasks.
Use 2 leading dashes and dash-separators for program options

This makes options consistent with most other applications, and easier
to type.
Rename org-based DN KEY_* env-vars to REQ_*

This naming convention accurately reflects that these are request
attributes, not "key" attributes.
Rename build-dh to gen-dh

This command generates DH params and isn't building or packaging
anything, so the new name reflects that.