Update ARCtrl and some additional dependencies

[kMutagene]

No description provided.

[kMutagene]

@HLWeil what do you think how robust such an update will be? this tool is used on every commit on every arc on the datahub.

[HLWeil]

As the current ARCtrl version is used in ARCitect, I would expect the read-in to be fairly robust.

But there might be Issues with very old ARCs
nfdi4plants/ARCCommander#240

[kMutagene]

i am mostly concerned with the json output. Ideally, we can use this update occasion to switch the output to RO crate.

So will

All ARCs -> Read -> RO Crate Json

Work? i mean we can and will still put empty json there on error, just asking how ready things are here

[HLWeil]

We could also allow both ISA and RO-Crate json via CLI args.

For RO-Crate I would first implement nfdi4plants/ARCtrl#344, and then use that function here.