Proposal update for dev containers/agentic standards + wdl command/bash tester

[jyang-broad]

This PR adds a couple things:

1. devcontainer setup: this is so we de-risk the AI from accidently doing bad things (tm)

2. AGENTS.md: adds an agents.md file

3. add bash checker - usage:
   python3 scripts/wdl_to_bash/wdl_to_bash_extractor.py pipeline.wdl --test

4. adds WIP local wdl smoke testing - usage:
   python3 scripts/run_test.py mt_coverage_merge --skip-cleanup
   4a. this is reliant on a testing folder located beside the mt_coverage_merge.wdl file that has mock data, mock dockers, and mock inputs.

[github-actions]

Remember to squash merge!

[github-actions]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

[github-actions]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

[github-actions]

Remember to squash merge!

[github-actions]

🔍Version Validation Results:

basename: missing operand
Try 'basename --help' for more information.
Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

[github-actions]

🔍Changelog Validation Results:

basename: missing operand
Try 'basename --help' for more information.
Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

[github-actions]

Remember to squash merge!

[github-actions]

🔍Version Validation Results:

basename: missing operand
Try 'basename --help' for more information.
Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

[github-actions]

🔍Changelog Validation Results:

basename: missing operand
Try 'basename --help' for more information.
Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

[github-actions]

Remember to squash merge!

[github-actions]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

[github-actions]

🔍Changelog Validation Results:

basename: missing operand
Try 'basename --help' for more information.
Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.