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Adversarial review of this PR found that pinning the runner format per script reopened issue #6896 one layer down. - `WorktreeSetupLaunch.shell` had been redefined to mean "the format the runner file was written in". `resolveSetupRunnerCommand` consumes it as "the shell that types the launch command", so a Git Bash terminal with a batch setup script produced `cmd.exe /c "C:\...\setup-runner.cmd"` typed into a bash pane, where MSYS rewrites the `/c` switch into a drive path: cmd opens interactively and setup never runs. `shell` is the terminal's family again; the runner file's .cmd/.sh extension carries the format, and a batch runner launched from a POSIX pane reuses the existing PowerShell ProcessStartInfo launcher. - The cmd runner dropped a leading `#!` line and ran the rest as batch, so a bash script reaching cmd (PowerShell/cmd terminal, or any SSH-to-Windows host) got its interpreter-agnostic prefix executed before failing mid-way. It now prints why and exits 1 without running anything. - A `#!` line's option flags were discarded: `#!/usr/bin/env -S bash -euo pipefail` lost pipefail because the runner is launched as `bash <path>`. The generated posix runner now replays declared flags via `set` and drops the duplicate interpreter line. - Docs cover the per-user setup command in repository hook settings, which goes through the same `#!` rule, and describe what the `#!` line does and does not select. Tests: composed launch command for a POSIX pane + cmd runner (hooks, shared runner command, setup sequencing gate, observed-setup signal), the cmd runner's shebang refusal, and shebang flag replay. Each fails with the source reverted.