Add @DeprecatedFeature annotation.

[cmnbroad]

This also fixes an issue where positional args were previously not showing up in command line help.

[codecov[bot]]

Codecov Report

Base: 76.66% // Head: 76.69% // Increases project coverage by +0.02% :tada:

Coverage data is based on head (89b9f4c) compared to base (7fe37aa). Patch coverage: 91.75% of modified lines in pull request are covered.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #187 +/- ## ============================================ + Coverage 76.66% 76.69% +0.02% - Complexity 744 762 +18 ============================================ Files 32 33 +1 Lines 2576 2609 +33 Branches 498 505 +7 ============================================ + Hits 1975 2001 +26 - Misses 406 409 +3 - Partials 195 199 +4 ``` | [Impacted Files](https://codecov.io/gh/broadinstitute/barclay/pull/187?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=broadinstitute) | Coverage Δ | | |---|---|---| | [...adinstitute/barclay/help/TemplateMapConstants.java](https://codecov.io/gh/broadinstitute/barclay/pull/187/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=broadinstitute#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvYmFyY2xheS9oZWxwL1RlbXBsYXRlTWFwQ29uc3RhbnRzLmphdmE=) | `0.00% <0.00%> (ø)` | | | [...roadinstitute/barclay/help/TemplateProperties.java](https://codecov.io/gh/broadinstitute/barclay/pull/187/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=broadinstitute#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvYmFyY2xheS9oZWxwL1RlbXBsYXRlUHJvcGVydGllcy5qYXZh) | `0.00% <ø> (ø)` | | | [...a/org/broadinstitute/barclay/help/DocWorkUnit.java](https://codecov.io/gh/broadinstitute/barclay/pull/187/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=broadinstitute#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvYmFyY2xheS9oZWxwL0RvY1dvcmtVbml0LmphdmE=) | `85.71% <66.66%> (-3.65%)` | :arrow_down: | | [...arclay/argparser/PositionalArgumentDefinition.java](https://codecov.io/gh/broadinstitute/barclay/pull/187/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=broadinstitute#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvYmFyY2xheS9hcmdwYXJzZXIvUG9zaXRpb25hbEFyZ3VtZW50RGVmaW5pdGlvbi5qYXZh) | `74.32% <85.00%> (+3.95%)` | :arrow_up: | | [...nstitute/barclay/argparser/ArgumentDefinition.java](https://codecov.io/gh/broadinstitute/barclay/pull/187/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=broadinstitute#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvYmFyY2xheS9hcmdwYXJzZXIvQXJndW1lbnREZWZpbml0aW9uLmphdmE=) | `74.61% <93.33%> (+2.44%)` | :arrow_up: | | [...e/barclay/argparser/CommandLineArgumentParser.java](https://codecov.io/gh/broadinstitute/barclay/pull/187/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=broadinstitute#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvYmFyY2xheS9hcmdwYXJzZXIvQ29tbWFuZExpbmVBcmd1bWVudFBhcnNlci5qYXZh) | `89.44% <100.00%> (+0.13%)` | :arrow_up: | | [...ute/barclay/argparser/NamedArgumentDefinition.java](https://codecov.io/gh/broadinstitute/barclay/pull/187/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=broadinstitute#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvYmFyY2xheS9hcmdwYXJzZXIvTmFtZWRBcmd1bWVudERlZmluaXRpb24uamF2YQ==) | `77.81% <100.00%> (-0.78%)` | :arrow_down: | | [...titute/barclay/help/DefaultDocWorkUnitHandler.java](https://codecov.io/gh/broadinstitute/barclay/pull/187/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=broadinstitute#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvYmFyY2xheS9oZWxwL0RlZmF1bHREb2NXb3JrVW5pdEhhbmRsZXIuamF2YQ==) | `73.66% <100.00%> (-0.46%)` | :arrow_down: | | [.../org/broadinstitute/barclay/help/GSONArgument.java](https://codecov.io/gh/broadinstitute/barclay/pull/187/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=broadinstitute#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvYmFyY2xheS9oZWxwL0dTT05Bcmd1bWVudC5qYXZh) | `100.00% <100.00%> (ø)` | | | [.../org/broadinstitute/barclay/help/GSONWorkUnit.java](https://codecov.io/gh/broadinstitute/barclay/pull/187/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=broadinstitute#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvYmFyY2xheS9oZWxwL0dTT05Xb3JrVW5pdC5qYXZh) | `100.00% <100.00%> (ø)` | | | ... and [5 more](https://codecov.io/gh/broadinstitute/barclay/pull/187/diff?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=broadinstitute) | | Help us with your feedback. 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[cmnbroad]

@droazen I can't recall any reason why this was left as draft. I think its ready for review.

[cmnbroad]

Sorry @lbergelson, I had to add one more commit based on testing with GATK. I messed up the command line display formatting when I factored out display code in this PR, which shows up spectacularly in GATK. We were outputting this:

instead of the output produced with this last commit:

[lbergelson]

@cmnbroad Ugh, good catch. Formatting things is hard.

[lbergelson]

@cmnbroad Good to merge.

[cmnbroad]

Thanks @lbergelson!