Users reported gx doctor failing hard on package script mismatches even when repair could resolve them. Root cause was a duplicate legacy doctor definition overriding the active repair-first flow in the command path.

This patch keeps the repair-first doctor as the only active doctor command, and aligns worktree dirty detection with normal untracked-file mode using git status --porcelain --untracked-files=normal --.

Constraint: Preserve existing doctor command UX and output contract for guarded repos
Rejected: Delete legacy doctor audit block entirely in this hotfix | larger refactor than needed for immediate behavior fix
Confidence: high
Scope-risk: narrow
Reversibility: clean
Directive: Do not introduce duplicate top-level command handlers with the same function name
Tested: node --check bin/multiagent-safety.js; npm test; node bin/multiagent-safety.js doctor --target /home/deadpool/Documents/recodee
Not-tested: npm publish/install path for this patch version