feat: migrate wdl-gauntlet to the new parser implementation.

[peterhuene]

This commit removes the use of the existing parser implementation in favor of the new implementation in wdl-gauntlet.

As a result, Arena.toml and Gauntlet.toml have been refreshed; in the case of Arena.toml, there's a ~10X increase in logged diagnostics due to the new parser implementation successfully parsing files that the existing parser implementation incorrectly parsed with errors.

Also added some wall-clock timing for the time spent analyzing a source file and an aggregate duration displayed at the end of gauntlet's output. From the before and after comparisons, the new parser implementation appears to be at least 20X faster in analyzing files, likely due to using logos for lexing and the new parser implementation does not backtrack like pest does.

Also added configuration for ignoring specific files so that task-templates.wdl can be excluded as it isn't expected to be valid WDL (it has non-WDL placeholders in it to serve as a template).

Once this merges and we're in consensus, removal of the existing parser implementation can begin.

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[a-frantz]

Was kicking tires. Noticed a regression in the PreambleComments rule. Alerting repo was aws-samples/amazon-omics-tutorials. They use our concept of preamble comments but after the version statement. This results in one diagnostic per line of a long block. One of the changes included in #61 was to report the entire span of problematic comments as one concern (as it was in the old parser).

Can we update the PreambleComments rule to report a multiline span? That should cut down the number of diagnostics coming out of that AWS repo, making them a candidate to add to Arena.toml (maybe, I haven't done a wc -l to see how many new ones they would add)

[a-frantz]

Another very similar case found in this files preamble: https://github.com/biowdl/tasks/blob/develop/deconstructsigs.wdl

We should similarly be reporting a multiline span instead of one per line

[peterhuene]

@a-frantz good catch. That should be easily fixed. Do you want me to include the fix in this PR?

[a-frantz]

Sure, if you say it's an easy one!

[peterhuene]

Question:

# BAD
# BAD



# BAD

Is that one diagnostic about the incorrect comments or two? Put another way, are the comments consecutive if they have only a single newline in separating whitespace or any number of blank lines inbetween?

[a-frantz]

Question:

# BAD
# BAD



# BAD

Is that one diagnostic about the incorrect comments or two? Put another way, are the comments consecutive if they have only a single newline in separating whitespace or any number of blank lines inbetween?

IMO one per "chunk" of trivia. Does that make sense?

[a-frantz]

Last comment I'll make 😅
Can we add getwilds/ww-vc-trio and getwilds/ww-star-deseq2 to Arena? Both are very small repos and add a limited number of diagnostics. Gives us a little more to work with without being overwhelming. And ww-vs-trio has one of the preamble cases I pointed out, so a good test case.

[peterhuene]

@a-frantz pushed up both changes.

[a-frantz]

Awesome work!