fix incorrect usage of add_handled_dependencies

[jakecoffman]

What are you trying to accomplish?

Finally got to the root cause of the issue I've been hunting, previous PRs for additional context:

• removing more of dependency_has_directory feature flag #10252
• revert changes to DependencyGroupChangeBatch #10228

The issue was caused by DependencySnapshot's methods needing current_directory being set beforehand, but several places we were calling add_handled_dependencies it wasn't set yet.

To fix that, I made a helper mark_group_handled which is appropriate to call in those places. It's also a good place to start using directory in the existing group PR data, but I'll save that for another PR.

This has also fixed a bad test vu-group-multidir-semver.txt had an incorrect second assertion. There are 4 dependencies across 2 directories, with a major and minor group all 4 should be updated in 2 PRs. This is fixed!

Anything you want to highlight for special attention from reviewers?

How will you know you've accomplished your goal?

I will manually test against our repo that was getting individual PRs when it should not have.

Checklist

• I have run the complete test suite to ensure all tests and linters pass.
• I have thoroughly tested my code changes to ensure they work as expected, including adding additional tests for new functionality.
• I have written clear and descriptive commit messages.
• I have provided a detailed description of the changes in the pull request, including the problem it addresses, how it fixes the problem, and any relevant details about the implementation.
• I have ensured that the code is well-documented and easy to understand.