Selective case update

[dnil]

From discussion with @rannick:

Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.
When cases are updated, either a long time is spent loading, or if extra keys are given on CLI to samples or cases, this is only stored in the scout db, not in e.g. housekeeper for future updates. This is made apparent by the current effort to update DNA cases with tomte RNA data.

Describe the solution you'd like
Instead of the current model with either cleanly loading everything from config, or adding extra files/keys, parse an update config and only adjust/load for values that actually changed.

At the same time as adding this, deprecate a bunch of odd separate and partially non-functional options on scout update case - e.g. all the vcf options.

Describe alternatives you've considered
Explicit field tags in the config, like update on the row. Checksums on each data file, reloading on update only if the checksum has changed.