Markdown integration

[magicDGS]

Markdown integration in the CLI help and documentation generation using commonmark-java. Includes:

• CLI: rendering to plain text fields in argparser annotations
• DocGen: rendering to HTML fields in argparser annotations and javadoc

[magicDGS]

Here you have the PR, @vdauwera!

[codecov-io]

Codecov Report

Merging #68 into master will increase coverage by 0.61%.
The diff coverage is 92.1%.

@@             Coverage Diff             @@
##             master     #68      +/-   ##
===========================================
+ Coverage     74.08%   74.7%   +0.61%     
- Complexity      517     530      +13     
===========================================
  Files            21      21              
  Lines          1999    2012      +13     
  Branches        412     412              
===========================================
+ Hits           1481    1503      +22     
+ Misses          346     344       -2     
+ Partials        172     165       -7

Impacted Files	Coverage Δ	Complexity Δ
...e/barclay/argparser/CommandLineArgumentParser.java	82.41% <100%> (+0.05%)	176 <0> (ø)	⬇️
...titute/barclay/help/DefaultDocWorkUnitHandler.java	73.8% <89.47%> (+2.16%)	79 <10> (+5)	⬆️
...roadinstitute/barclay/help/DocWorkUnitHandler.java	89.47% <93.33%> (+22.8%)	10 <8> (+7)	⬆️
...va/org/broadinstitute/barclay/help/HelpDoclet.java	75.14% <0%> (+0.59%)	47% <0%> (+1%)	⬆️

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[vdauwera]

Thanks @magicDGS !

The functionality looks great to me.

@cmnbroad What do you think?

[cmnbroad]

I haven't had a chance to look at this in detail yet (I'll get to it as soon as I can, but realistically it won't be until we get beta finished). One high-level request is that we find a way to incrementally unit-test new functionality like this at a granular level. We currently only have coarse-grained, file-based integration tests, and I'd like to find a way to avoid proliferating a new set of test files with each new feature, in addition to changing many/all of the existing ones. @magicDGS any thoughts on how we can address that ?

[magicDGS]

I open an issue (#71) to discuss how to change the docgen tests. Let's keep this PR for the Markdown support, which may be also generate some discussion...