ElastixWrapper refactoring

[K-Meech]

@tischi this is a rather massive pull request - so happy to discuss/ restructure it if you'd like! All commands should remain the same, so there won't be any changes for users - only backend changes. The main aim was to separate the command line functionality so it could be called more easily from other code.

Main changes:

• metaimage (mhd) reading and writing is split into another repo: https://github.com/embl-cba/metaimage-io . This would need to be shipped with the update site instead.
• everything to do with calling elastix / transformix on the command line is split from the rest. This means it can be called very easily independently of staging files.
• Elastix and transformix functionality is separated (on command line side and in wrappers and settings)
• Separated generation of default parameters from the class that holds the current parameters (again, easier to call from external code)
• Separated the staging functionality into its own class
• Separated all the bdv display functionality into its own class

[tischi]

This looks really ❤️ ly ! Seriously great work!

I would just merge it as is. @K-Meech you can also do it (do you have the rights?). If you merge it please inform: https://forum.image.sc/t/exception-when-trying-to-run-elastix/30375 (He however did not seem to have forked it yet).

(@bogovicj @NicoKiaru: @K-Meech did a great job in making the code in this repo more modular, maybe this is also interesting for your usage, in case you are using the Java API of this repo, are you?)

[NicoKiaru]

This looks really great! I'm not using it for now, I could switch when I'll have time, but it's not on my priority list. . Probably when I'll need 3D registration, I'm going to 'reopen the case'.

[K-Meech]

Great!! @tischi I don't think I have the rights to merge - you'd have to add me as a collaborator.