Agents (executor, verifier, planner) were writing markdown files via Bash heredocs. When approved, Claude Code persisted the entire heredoc as a permission entry, breaking settings.local.json on next launch. Added explicit "use Write tool" directives to all three agents and added missing Write tool to gsd-verifier's tool list. Closes #526 Closes #491 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>