konard/test-hello-world-019bea4f-95dc-702e-8887-c1f4975529b6@400ab4c

Instead by default we should use --gitkeep-file for --tool agent, and --claude-file should be by default disabled for --tool agent.

We also need update docs, and make sure we write that different tools have different default values for corresponding options.

Please download all logs and data related about the issue to this repository, make sure we compile that data to ./docs/case-studies/issue-{id} folder, and use it to do deep case study analysis (also make sure to search online for additional facts and data), in which we will reconstruct timeline/sequence of events, find root causes of the problem, and propose possible solutions.