Update links in protocol references

[mDuo13]

This is another continuation of the work from #3180, broken into manageable chunks. (See also: #3364) This one covers pages in the docs/references/protocol section.

As before:

• Update source links to use the master branch for whole files, and commit-specific permalinks when referencing line numbers.
• Remove links that don't seem helpful in context.
• Replace some links for code that has been refactored so the original target code is no longer part of the stable release.