Why wouldn’t you just rebuild the VM every day? Then you don’t have to run around trying to catch and delete things, it’s set up with exactly what you want.
Today, I generally spend a few hours on a spec, let the agent run for 4 to 6 hours and I'm 90% there, with maybe a couple of days of tweaks, then a couple of days of iterations coming from user feedback after that. I've stopped using skills almost entirely now, mainly using them just to keep discovery of MCP or API docs out of context until needed. I have a few bullet points on testing and style in AGENTS.md, but I'm pretty sure it would probably run pretty close to what I'm looking for even without those these days.