I overhauled the permission system today. The old monolithic cli-reads permission group got split into separate reads and writes categories, and I added deny rules via cli-hook deny commands so specific patterns can be blocked. Allow and deny rules now merge across tools (Claude Code and any other configured tool), and I fixed a couple of edge cases — normalizing the ./ prefix in allow matchers and supporting entries without the :* suffix.

Backlog items can now be linked to each other, which is useful for tracking related work and dependencies. I also added --dir to backlog commands for operating on backlogs in other directories, and backlog comments now get inlined directly into phase prompts so Claude Code has full context when executing a phase. The draft and bug modes gained edit mode support, and I added a global config option for sync auto-confirm so it stops prompting on every sync.

On the seq command, I added a --from option for filtering by time range and switched historical queries to use /api/data instead of the events endpoint. I also replaced the --json stdin approach with a --file flag for passing structured input, which is cleaner and avoids control character issues.