chore: Refactor out usage of --all and --graph wrappers where they aren't needed

[yhakbar]

Description

Refactors out usage of the --all and --graph wrappers in commands besides run so that we're not coupling the behavior so tightly.

TODOs

Read the Gruntwork contribution guidelines.

• I authored this code entirely myself
• I am submitting code based on open source software (e.g. MIT, MPL-2.0, Apache)]
• I am adding or upgrading a dependency or adapted code and confirm it has a compatible open source license
• Update the docs.
• Run the relevant tests successfully, including pre-commit checks.
• Include release notes. If this PR is backward incompatible, include a migration guide.

Release Notes (draft)

Added / Removed / Updated [X].

Migration Guide

[vercel]

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Project	Deployment	Preview	Comments	Updated (UTC)
terragrunt-docs	Ready	Preview	Comment	Nov 5, 2025 10:06pm

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✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch chore/refactoring-out-usage-of-run-for-non-run-commands

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