manifest: update to match metadata documentation

[ES-Alexander]

• We have new metadata recommendations that have not yet been implemented (e.g. the new type and tags fields, and some of the existing link fields being consolidated into the new links field).
• We're also not including the website field in each RepositoryEntry.
• We're planning to rename the company fields to maintainer fields instead, which is a breaking change

We should update consolidate.py appropriately.