Stale __source-probe worktrees were being reused as if they were the branch's real worktree, which let leaked probes block finish and surface as fake repos in editor repo scans. This patch removes stale probes before finish, treats probe paths as temporary during prune even when they track agent branches, and rewrites doctor conflict guidance so operators rebase the real branch in a normal worktree.

Constraint: gx doctor and gx branch finish still need a temporary probe when no live branch worktree exists
Rejected: Keep telling users to continue rebases inside __source-probe worktrees | conflicts with the cleanup contract and leaves fake repos behind
Confidence: high
Scope-risk: moderate
Reversibility: clean
Directive: Treat __source-probe-* paths as disposable plumbing; do not promote them to operator-facing workflow state again
Tested: bash -n scripts/agent-branch-finish.sh scripts/agent-worktree-prune.sh templates/scripts/agent-branch-finish.sh templates/scripts/agent-worktree-prune.sh; node --test test/doctor.test.js test/worktree.test.js test/finish.test.js
Not-tested: gx branch finish --via-pr --wait-for-merge against live GitHub