[Noir, C++, TS] All side-effect objects should be paired with a counter

[dbanks12]

Blocked by #864

1. read_requests
2. new_commitments
3. new_nullifiers
4. public_call_stack entries
5. new_l2_to_l1_messages (unsure of this one, but i think we should give it an order to be safe?)
6. encrypted_log_preimages (these are encrypted notes to go into ethereum calldata)
7. unencrypted_log_preimages (these are like regular ethereum events)

Since this is a pretty large task already, consider breaking this up!

This makes a lot of changes and could lead to merge hell if it takes too long! Be sure to do #864 first to minimize time spent on this.