fixed legacy references to pybee

[jess010]

I've updated legacy pybee references present in the batavia repo Fixes outdated references, including some that result in broken links. I haven't raised an issue for this, but can if that is considered useful. ## PR Checklist:

• [] All new features have been tested - N/A, no change to non-doc features, have tested a sample of updated links manually though.
• [] All new features have been documented - N/A, no new code added
• [x] I have read the CONTRIBUTING.md file
• [x] I will abide by the code of conduct

[danyeaw]

@jess010 This looks great thanks! :heart: