Description

Fixes #4659

The problem is that the index was not retained when doing an upgrade, so that meant it was using the wrong index to do the dependency upgrade. I also though a TryFrom from a tuple that does merging is really unclear, so I made this into a function on the struct itself. Now we correctly take the index into account when updating.

How Has This Been Tested?

I've not tested it manually but I feel the automated test is essentially the user-test in this case. I tested that it fails without this change and succeeds with this change.

AI Disclosure

• This PR contains AI-generated content.
  • [] I have tested any AI-generated content in my PR.
  • I take responsibility for any AI-generated content in my PR.

Tools: {e.g., Claude, Codex, GitHub Copilot, ChatGPT, etc.}

Checklist:

• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• I have added sufficient tests to cover my changes.
• I have verified that changes that would impact the JSON schema have been made in schema/model.py.