Runner workspace publication reuses stale post-squash branch history

[chubes4]

Problem

A runner workspace configured with a canonical publication branch reused the remote branch history left behind after an earlier squash merge instead of starting from the requested current base ref. The model change and deterministic verification succeeded, but the resulting PR included historical commits, stale generated documentation, and merge conflicts.

Evidence

• Successful hosted run: https://github.com/Automattic/agents-api/actions/runs/29745532621
• Polluted publication PR: Run Docs Agent agents-api#444
• Requested base: main at b134d5767efe0156c05f70fe1996b7665eff8831
• Configured branch: docs-agent/agents-api-docs-upkeep
• Actual published branch: docs-agent/agents-api-docs-upkeepdocs-agent-technical-maintenance
• New isolated task commit: 6f2025638e662f48ab39eeb3d26c78d8fb4d80e1
• PR also retained three commits from the branch used by earlier PR agent runtime: require structured completion outcome from sandbox agents #430, which had been squash-merged.

Expected

Each runner publication starts from the declared from/base revision. Existing canonical branches must either be proven fast-forward-compatible with that base or replaced through a safe fresh-branch strategy. Post-squash historical commits must not reappear in a later PR.

Acceptance criteria

1. Reusing a configured publication branch cannot carry commits absent from the declared base.
2. Existing branch divergence is detected before agent execution or publication.
3. The runner creates a fresh collision-safe branch or returns a deterministic actionable failure.
4. Tests cover an existing branch whose prior commits were squash-merged into base.
5. Publication output reports the exact effective branch and base SHA.