Agentic Research Workflow

.bin/agent --client codex

Project-local workflow for research tasks (writing, literature scouting, computation, review) with the user in control.

1. cd into this repo and open Codex UI (recommended).
2. In Codex UI, run shell commands with !.
3. Route requests with quotes: !bart "<free text request>".
4. !bart is suggest-only by default: it prints ranked candidates and requires an explicit pick.
5. One-step start+run: !bart "<request>" --pick 1 --run.
6. Successful runs always stage to GATE/staged/<task_id>/<skill>/....
7. Default mode (AGENT_MODE=off) never auto-promotes; promotion requires explicit confirmation: PROMOTE_TO_USER? [y/N].
8. Canonical promote command is ./AGENTS/runtime/promote_to_user.sh --task <task_id>.
9. Global mode can be enabled explicitly with ./bin/agenthub run ... --agent-mode --auto-promote-user.
10. In non-interactive runs, promotion requires --yes --allow-user-write-noninteractive; otherwise promotion is skipped.
11. USER/ is canonical and is never auto-written unless explicitly promoted.
12. Optional dangerous routing mode: !./bart --full-agent "<request>" (auto-picks and executes).
13. If you want zero agent flow, do not run ./bart or ./bin/agenthub; use your tools directly.

Example flow:

• !bart "update metadata" --pick 1 --start
• !bin/agenthub run --task <task_id> --yes
• respond to PROMOTE_TO_USER? [y/N] or run ./bin/agenthub promote --task <task_id> later.