Skip catalog protocol when using directory configuration in monorepos

[robaiken]

What are you trying to accomplish?

When updating individual repositories within a monorepo using the directory configuration, we want to skip the catalog: protocol. This change improves the handling of monorepo dependency updates by ensuring Dependabot correctly processes directory-specific updates without being affected by the catalog protocol.

Anything you want to highlight for special attention from reviewers?

The main change focuses on the protocol handling logic. I chose to skip the catalog protocol specifically for directory updates since these are meant to operate on isolated parts of the repository, and the catalog protocol isn't necessary in this context. This approach ensures clean, targeted updates for individual packages within monorepos.

How will you know you've accomplished your goal?

Users can successfully process updates for specific directories in their monorepo. The "no change" errors previously triggered by catalog versions no longer block these updates

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.