I would also include in my billing a 30 minute lunch over an 8 hour day, which is the minimum mandated by local (Canadian) labour law, and I would bill for any incoming calls and email that is related to the project I'm working on.
I'm definitely aware of how different my time feels when I'm billing, and I've tried to relax a bit. I think billing daily or weekly is always better than hourly.
That said I understand getting to daily or weekly rates can really let your rates take off, and you don't have to worry about what time you're on the clock in the same way.
I get being hesitant to bill for certain kinds of troubleshooting, but I think it comes down a lot to what the scope of the project is. If I'm on something that is multiple weeks of work, and I'm dealing with a problem that I would be encountering and would be expected to solve if I were working full-time, then it's billable.
If you bill daily or weekly, then great. If you bill hourly, then the only way this is okay is if you put "30 minutes lunch" on your bill and show that you're charging for it. There's a reason why it's very very hard to bill for 8 hours of work in a day, and that's because you don't work for 8 hours.
If your client understands and expects to be billed for lunch, and your client is paying for your time from 9-5, then it's reasonable. (But that would be a rare situation, normally that would be very temporary, or become a full-time salaried position). If your client is paying for your work on an hourly basis, and has not explicitly agreed to pay for your lunch, then billing for it should be off limits.
For most hourly contract work, lunch is on your own time, not billable hours. I'd be pissed if my lawyer were billing me for lunch, it would be downright dishonest.
As far as debugging, I assumed the parent's comment was talking about debugging his own tools, for example a debugging activity that applies to all his clients, or to himself, rather than time spent on project specific triage. If I'm working directly on the project, I bill for it. If I'm working on something that is indirect and/or not solely for the project's benefit, then I don't.
The overhead of recording time and dealing with every call and email ends up being - for me - way too much time/recordkeeping. Scheduled calls/meetings, yes. Someone has a 3 minute call where I can answer a followup question - I just answer it. "But you'll be interrupted all the time with 3 minute calls!" - except, if I'm too busy or don't want to be distracted... I just don't take the call.
Daily/weekly can be, if the clients are OK with that too. I've found some that aren't. along with that, I typically have multiple projects running simultaneously, and I can't - in my mind - ethically charge for a 'day' if I've split my time on 2-3 projects that day.
I don't like charging for time at all, really, but some orgs aren't really set up to handle any other mode of work (and/or, want flexibility in change, so time may be the least unfair approach).