[pigeon] Enable NNBD in tool

[stuartmorgan]

Opts Pigeon into running in NNBD mode. All of the code had already been converted.

Also updates a legacy Dart commands (dart pub run) in the test script to the modern version.

Pre-launch Checklist

• I read the Contributor Guide and followed the process outlined there for submitting PRs.
• I read the Tree Hygiene wiki page, which explains my responsibilities.
• I read and followed the relevant style guides and ran the auto-formatter. (Unlike the flutter/flutter repo, the flutter/packages repo does use dart format.)
• I signed the CLA.
• The title of the PR starts with the name of the package surrounded by square brackets, e.g. [shared_preferences]
• I listed at least one issue that this PR fixes in the description above.
• I updated pubspec.yaml with an appropriate new version according to the pub versioning philosophy, or this PR is exempt from version changes.
• I updated CHANGELOG.md to add a description of the change, following repository CHANGELOG style.
• I updated/added relevant documentation (doc comments with ///).
• I added new tests to check the change I am making, or this PR is test-exempt.
• All existing and new tests are passing.

[flutter-dashboard]

It looks like this pull request may not have tests. Please make sure to add tests before merging. If you need an exemption to this rule, contact Hixie on the #hackers channel in Chat (don't just cc him here, he won't see it! He's on Discord!).

If you are not sure if you need tests, consider this rule of thumb: the purpose of a test is to make sure someone doesn't accidentally revert the fix. Ask yourself, is there anything in your PR that you feel it is important we not accidentally revert back to how it was before your fix?

Reviewers: Read the Tree Hygiene page and make sure this patch meets those guidelines before LGTMing.

[Hixie]

test-exempt: configuration change

[gaaclarke]

lgtm