Prepare for global reference-transaction hook executions

While starting to work on enabling the reference-transaction hook globally, I noticed we still weren't actually executing hooks. This mostly boils down to the fact that we don't pass core.hooksPath. Adding this is blowing up most of our testsuite though as now all modifying Git operations require the hook service to be set up. I've thus decided to create a preparatory MR for the first batch of modifications required to make reftx hooks work globally as the actual changes will be quite involved.

Part of #3310 (closed)