pulsarify all tools in the repo

[martenson]

pulsar needs to explicitly know about the files included in the command, this PR adds this information to all tools in the repo that are missing it (some already had it)

While having a look a this I also found some minor inconsistencies in requirements and syntax, check the later commits for details.

closes #279

FOR CONTRIBUTOR:

• - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• - License permits unrestricted use (educational + commercial)
• - This PR adds a new tool or tool collection
• - This PR updates an existing tool or tool collection
• - This PR does something else (explain below)

[bgruening]

Thanks @martenson. Can you maybe come up with a small script to detect those tools. We probably want to add this to more tools.

[martenson]

@bgruening done

[bgruening]

That looks great!

[hechth]

@martenson is there still an issue or do you have some idea why the tests are failing?

[martenson]

@hechth I am not aware of any issue and I do not have access to this repo to troubleshoot tests.

[bgruening]

Many tools' linting is failing because we are touching many tools now. Of course, it would be nice to fix those, but I can also understand if you just want to merge it.

[martenson]

I took care to not break the linting with my modifications and I do not have the availability to fully re-lint all tools I am fixing here.

[hechth]

@martenson I'll see what I can do to fix tests and linting etc.

[bernt-matthias]

With #282 CI should run again.

• tool linting problems can be added to a .lint_skip file, e.g. see here
• problems with R linting can be fixed using the styler.R tool (from the above PR) .. but deployment should also work without fix

[hechth]

@bernt-matthias I am currently working on fixing the linting and testing, to also give the tools some general update.

[martenson]

rebased on top of #282 -- thank you @bernt-matthias !

[bernt-matthias]

Can someone approve the workflow run?

[hechth]

this is superceded by #283