This is one of those moments where someone is theory own worst enemy. The expectation for people to bottle up their feelings and sit there in annoyance is silly. There are only two basic scenarios here. The cause of the annoyance mainly sits with...
1. Jim.
2. John Ousterhout.
3. Some unidentified cause.
The proper approach is to think carefully about whether it is case 2. If it is, stop feeling annoyed - the annoyance is harming the self and the relationship for no reason. It is an illusion that can only cause trouble.
Most of the time that is the end of it. However, sometimes it is a case 1 or 3. Then it is perfectly fine to sit down with Jim and talk feelings. Just do it. Learn to make it sound natural and stilted and people only notice that you seem really easy to talk to. Figure out whether it is case 1 or 3 and whether it can just be resolved on the spot. Nobody is helped by bottling even minor things up. Learn to live a comfortable life.
It drives me crazy when I find out people just sit there and don't tell me when I'm upsetting them. Communication, my men! If you can't fix it in your own head, get other people involved and talk it through.
Plug for Marshall Rosenberg and Nonviolent Communication. This stuff really can be reduced to an algorithm as long as it accompanies a relentlessly nonjudgemental mindset and a tolerance for not getting your own way.