Migrated from Method backlog

This issue was created from a legacy filesystem backlog card. GitHub Issues are now the live work tracker; repository docs remain Method evidence.

Source backlog: docs/method/backlog/cool-ideas/PROCESS_doctor-policy-toleration-config.md
Original lane: cool-ideas
Original legend: PROCESS
Original priority: low

Original backlog card

Doctor Policy Toleration Config

method doctor is intentionally opinionated, but some repos will make
deliberate choices that should not read like operational failure. A
simple example is git hooks: some repos will intentionally rely on CI
only, while others may treat missing hooks as a real problem.

Right now METHOD can only emit its built-in judgment. That is clean, but
it forces every repo into the same operational posture even when the
check result is true but not actionable for that repo.

Proposed Contract

• Config surface:
  allow a bounded doctor policy block in .method.json, such as
  doctor: { tolerations: [...] }, for named checks or issue codes.
• Scope:
  tolerations may only downgrade or reclassify known doctor findings.
  They must not disable arbitrary code paths or hide unknown failures.
• Output truth:
  doctor output must still include the underlying issue and identify any
  active toleration, for example by adding tolerated: true or
  effective_severity.
• First practical target:
  support repo choices such as "missing git hooks are informational
  here" without forcing downstream agents or humans to special-case the
  repo manually.

Non-goals

• Turn doctor into a free-form lint-config framework.
• Let repos hide hard structural failures silently.
• Replace CI or review policy with doctor configuration alone.