bug(unic-archon-dlc, upstream: Archon): a folder project registered on a parent directory swallows every child clone, and doctor passes it #492

Observed

~/.archon/archon.db remote_agent_codebases held one row, <customer> | /home/otf/Sites/<customer> | kind: folder | default_branch: (empty), registered by the maintainer through the Archon Serve UI by mistake (meant the clone). ~/Sites/<customer> is a customer folder with three clones and is not a repository. Effects: a dispatch from inside DXP-DesignSystem printed "Folder project — running in place (no worktree isolation)" and ran on develop in the clone; worktree.baseBranch: develop from the committed .archon/config.yaml was never read (default_branch empty); listChildRepos made the row cover all three Consumer clones. archon doctor reported ✓ Folder project: "<customer>" (runs in place) — 3 contained repo(s) … All checks passed. No CLI verb removes a codebase.

Why it matters

One mis-click removes isolation for every repository under a customer folder, and the health check endorses it. In-place, the Box commits on develop and open-pr cannot push past the pre-push guard, so the leg would end without a PR.

Evidence

• Findings register, § "G. What run 3 taught about the instrument", row G3: https://github.com/unic/unic-agents-plugins/blob/bcf688a/docs/research/2026-08-31-dlc-run-2-findings.md
• Run record and harvested artefacts: ~/Desktop/run3-parked/ on the maintainer's machine (run record § the first dispatch; archon doctor output quoted there)
• Dispatch record: #457 from comment 5698289748 down

Not decided

• Upstream: a repo project inside a folder project's tree should win, or doctor should warn when a folder project contains git repositories.
• Consumer doc row: verify the codebase row (kind, default_cwd, default_branch) before any dispatch on a new machine; a dispatch header saying "running in place" means abandon.

Filed 2026-09-17 by wayfinder-orchestrator-10 from run 3's measurements. needs-specs: grill before dispatch.