Include more sources to avoid lowest bound warning (#9644)
In https://github.com/astral-sh/uv/issues/8155#issuecomment-2508969900,
resolution lowest was complaining about missing lower bounds for a
pacakge, even though the package had a URL, too:
```
uv pip install dist/pymatgen-2024.10.3.tar.gz pymatgen[ci,optional] --resolution=lowest
```
The error was raised from `pymatgen[ci,optional]`, because we were
looking at it before looking at the "URL"
`dist/pymatgen-2024.10.3.tar.gz`.
I've also added constraints and overrides to the bounds lookup, since
they are missing from the dependency graph.
Fixes #8155 (again)
