Add a flag to choose which manifests to enable

[43081j]

We currently have 3 manifests:

• native
• preferred
• micro-utilities

The CLI just uses the all alias when running analysis and migrations today. We should instead have a flag which defaults to all but can be set to one or more of these manifests.

e.g.

--categories=native
--categories=native,preferred
--categories=all

This would then be used both by the analysis command and the migration command