[Documentation] fix broken links

[sage-wright]

This PR closes #624.

🗑️ This dev branch should be deleted after merging to main.

🧠 Summary

The documentation had several broken links; this PR corrects them and updates any PHBG & PHVG links to the appropriate PHB ones.

⚡ Impacted Workflows/Tasks

This PR may lead to different results in pre-existing outputs: Yes/No

This PR uses an element that could cause duplicate runs to have different results: Yes/No

🛠️ Changes

⚙️ Algorithm

➡️ Inputs

⬅️ Outputs

🧪 Testing

Suggested Scenarios for Reviewer to Test

🔬 Final Developer Checklist

• The workflow/task has been tested and results, including file contents, are as anticipated
• The CI/CD has been adjusted and tests are passing (Theiagen developers)
• Code changes follow the style guide
• Documentation and/or workflow diagrams have been updated if applicable (Theiagen developers only)

🎯 Reviewer Checklist

• All changed results have been confirmed
• You have tested the PR appropriately (see the testing guide for more information)
• All code adheres to the style guide
• MD5 sums have been updated
• The PR author has addressed all comments
• The documentation has been updated