Extension of Broekx: the shared git index

Extends Ruben Broekx, “AI Agents Need Their Own Desk, and Git Worktrees Give Them One” (Towards Data Science, 2026-04-18), which named the problem this note builds on. Read his piece first.

Claim: Broekx’s “desk” is right, and the hazard reaches one layer deeper than his telling. He shows that you and the agent sharing one working directory is dangerous — the agent edits while you edit, then reverts the changes it does not recognize — and that a git worktree, with its own branch and its own ports, gives each of you a separate desk. The layer underneath is the git staging area: even at one desk you share a single index, and an unscoped commit sweeps your half-staged work into the agent’s commit. A worktree fixes the working tree; it does not fix a plain “commit everything.”

What Broekx already established

The desk metaphor, and the human-versus-agent framing (not agent-versus- agent): a human making small edits while the agent runs, and the agent overwriting or reverting them because it has no memory of them. His fix is a worktree per agent — a second window on the same project, locked to its own branch — plus a per-worktree port offset so two dev servers do not fight over one port. All of that is his, and it is correct.

The part this adds — the shared index

The staging area is shared even within a single checkout, and it is not what a worktree isolates. The incident: I was staging my own changes by hand for a separate, half-finished commit while a session worked in the same tree. The session ran a plain “commit everything currently staged,” and my staged work went into its commit alongside its own. Nothing warned either of us. This is not a dirty-working-tree edit or a branch switch — the failure paths Broekx’s worktrees prevent — it is the index itself, and an unscoped commit reaches it whether or not you are on separate desks.

The rule

Take Broekx’s worktree as the baseline, then add two things it does not cover:

• Commit with explicit file lists — git commit -- path/to/file — never “commit everything” or git add -A, whenever a human might be staging in the same index.
• Keep your own processes on ports the agent will not reuse (his port-offset logic handles the agent’s side; make sure yours is out of its range too).

The through-line is his, one step further: treat anything you and the agent both touch as shared, changeable state — the working tree, the index, the ports — and the agent will not warn you, because from inside the session it has the desk to itself.

Prior art

Ruben Broekx, “AI Agents Need Their Own Desk…” (Towards Data Science, 2026-04-18) — the direct parent, verified: the desk framing, human-versus- agent, worktrees, and per-worktree ports are all his. Two Claude Code incident reports (GitHub anthropics/claude-code #37888 and #55024) show the same “acts as if alone, overwrites, no warning” dynamic through git checkout -- ., a different destructive path than the index sweep. A steipete gist prescribes explicit-file commits, framed for agent-to-agent coordination. Not found in the sweep: the shared-staging-index sweep between a human hand-staging and an agent’s unscoped commit, as distinct from the shared working tree — the one increment this note claims on top of Broekx. Connects to the session has no concurrency model: the other worker sharing your state can be you.