doc/dev: update logging conventions, align existing usage

Created by: bobheadxi

Outlines some logging conventions based on our recent migration work, and update some existing callsites to align with the new recommendations

The main document to review is doc/dev/how-to/add_logging.md

Closes https://github.com/sourcegraph/sourcegraph/issues/36734

Test plan

n/a, docs and minor logging usage changes but nothing major