Add linter exceptions for all linters that are currently failing

[bernt-matthias]

And re-enable warn as linter fail level.

It's like a TODO list :)

      1 HelpMissing
      1 InputsDataFormat
      1 InputsDataOptionsFiltersType
      1 InputsSelectDynamicOptions
      1 InputsSelectOptionsDeprecatedAttr
      1 RequirementVersionMissing
      1 ValidatorExpression
      1 ValidatorExpressionFuture
      2 InputsDataOptionsFilterAttribFiltersType
      2 InputsDataOptionsFiltersRef
      2 InputsNameDuplicateOutput
      2 InputsSelectOptionDuplicateValue
      2 OutputsNameDuplicated
      2 OutputsNameInvalidCheetah
      2 TestsOutputCompareAttrib
      2 ToolIDWhitespace
      2 XSD
      3 CommandTODO
      3 EDAMTermsValid
      3 InputsMissing
      3 TestsExpectNumOutputsFailing
      4 ConditionalWhenMissing
      4 InputsBoolDistinctValues
      4 InputsNameDuplicate
      4 InputsSelectOptionDuplicateText
      5 HelpInvalidRST
      6 HelpEmpty
      9 OutputsLabelDuplicatedNoFilter
     13 ConditionalParamTypeBool
     14 TestsMissing
     15 ToolVersionPEP404
     18 OutputsLabelDuplicatedFilter
     19 TestsParamInInputs
     29 CitationsNoValid
     32 CitationsMissing
     41 InputsNameRedundantArgument
     73 TestsExpectNumOutputs
    103 XMLOrder

Should replace #5650

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)

[bernt-matthias]

The remaining tool linter errors are all due to linters defined in planemo (working in it: galaxyproject/planemo#1472)

Tool tests won't finish with 4 chunks (and likely there fill be failing tests anyway).

I will fix the python linter problems.

[bgruening]

Do you want me to fix a few other stuff here or should we merge that and fix other stuff later?

If we merge this PR, so we cancel the CI or do we deploy?

[bernt-matthias]

If we merge this PR, so we cancel the CI or do we deploy?

I would not deploy. Since we do not change any tools (I should undo the changes to py and xml files and but them in a separate PR)

Do you want me to fix a few other stuff here or should we merge that and fix other stuff later?

I would put any other changes to a separate PRs.

[bernt-matthias]

The XSD errors are maybe due to a bug: galaxyproject/galaxy#18605

[bgruening]

@bernt-matthias please also have a look at bernt-matthias#107 ... not sure where it should go. Please let me know how you want to have those fixes.

[bgruening]

All the remaining failures are URLs that are not valid anymore.

[mvdbeek]

Awesome, thanks a lot!

[mvdbeek]

Attention: deployment skipped!

https://github.com/galaxyproject/tools-iuc/actions/runs/10719699458