lib/repo: Add MT support for transaction_set_ref(), clarify MT rules

lib/repo: Add MT support for transaction_set_ref(), clarify MT rules

For rpm-ostree I'd like to do importing in parallel with threads; the code is
*almost* ready for that except today it calls
`ostree_repo_transaction_set_ref()`.

Looking at the code, there's really a "transaction" struct here,
not just stats.  Let's lift that struct out, and move the refs
into it under the existing lock.

Clarify the documentation around multithreading for various functions.

Closes: #1358
Approved by: jlebon