Make nf-core modules lint use new config file

[sersorrel]

Previously nf-core modules lint would use a weird mixture of .nf-core-lint.yml (deprecated) and .nf-core.yml; I believe this PR removes all references to the former, except for the code in nf_core/utils.py that prints a warning if only the deprecated file is present.

For example, running nf-core modules lint fastqc on a freshly-created repo with the fastqc module shows a warning about fastqc being out of date, even with the following .nf-core.yml:

repository_type: pipeline
lint:
  main_nf: false

(if you instead put that lint config in .nf-core-lint.yml, you get... a weird crash "AttributeError: 'NFCoreModule' object has no attribute 'process_name'", but you do also get "INFO Ignoring lint test: main_nf".)

With this PR, the deprecated config file is ignored (like the rest of the lint commands), and you can only ignore the lint/cause the crash by including the lint config in .nf-core.yml.

I'm not sure how to write a test for this – if it's worth doing so I can give it a go (I guess some relevant existing tests are probably in tests/modules/lint.py?)

Fixes #2212

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!

[codecov]

Codecov Report

Merging #2221 (dfe2057) into dev (f3b5d1e) will decrease coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##              dev    #2221      +/-   ##
==========================================
- Coverage   71.95%   71.95%   -0.01%     
==========================================
  Files          77       77              
  Lines        8363     8358       -5     
==========================================
- Hits         6018     6014       -4     
+ Misses       2345     2344       -1     

Impacted Files	Coverage Δ
nf_core/__main__.py	58.81% <ø> (ø)
nf_core/lint/nextflow_config.py	77.45% <ø> (ø)
nf_core/components/components_command.py	71.32% <100.00%> (-0.30%)	⬇️

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[mirpedrol]

looks good 🙂