[Fix] multi-directory grouped updates sometimes create ungrouped PRs

[Nishnha]

What are you trying to accomplish?

Depends on #9988
This PR is stacked on top of #9988

Multi-directory grouped updates sometimes create ungrouped PRs because the #run_ungrouped_dependency_updates method relied on some old assumptions that have changed.

#run_ungrouped_dependency_updates makes use of DependencySnapshot#ungrouped_dependencies to check which dependencies do not belong to a group and require an individual PR.
This used to work, but we recently changed the way we calculate if a dependency belongs to a group with the introduction of multi-directory updates.

When Dependabot could only update 1 directory at a time, marking a dependency as "handled" with DependencySnapshot#add_handled_dependencies meant that it had been processed.

When we added multi-directory updates, we kept track of handled_dependencies per directory in case we handle a dependency in one directory and don't skip over it in a later directory.

This meant that when we changed the current_directory in the DirectorySnapshot, we lost the list of handled_dependencies, so dependencies belonging to an existing pull request group are not considered handled and are included in the ungrouped_dependencies list.

To account for this, this PR introduces DependencySnapshot#add_handled_group_dependencies and DependencySnapshot#handled_group_dependencies to mark every dependency in a group as handled across all directories and retrieve them.

Anything you want to highlight for special attention from reviewers?

This work depends on a few other PRs which also share the :dependency_has_directory feature flag. These other PRs add in a directory field to Dependabot::Dependency that this PR uses to track which dependencies are handled.

How will you know you've accomplished your goal?

We have a silent ecosystem test in this PR. This is also feature flagged so we can test it out on our test repo.

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.

[Nishnha]

I think we can still use the specs and silent ecosystem tests from #9610 in this