[tech-debt] format:check does not cover files outside workspace packages (.pair/**, scripts/**, root-level JSON)

[rucka]

Story Statement

As a contributor trusting pnpm format:check
I want the formatting check to cover the files that live outside workspace packages
So that "the gate checks formatting" means the whole repo, not only apps/* and packages/*

Epic Context

Parent Epic: repo tooling / quality gates (no epic — standalone tech debt)
Status: Todo
Priority: P2 (Could-Have)

Problem

format:check = pnpm prettier:check && pnpm mdlint:check, and:

• prettier:check is turbo prettier:check — turbo <task> only runs tasks in workspace members (apps/*, packages/*, tools/*). Files at the repo root and in non-workspace dirs are never prettier-checked: root package.json, turbo.json, .jscpd.json, .claude/**/*.json, scripts/**.
• mdlint:check adds markdownlint-check.sh '*.md' — a non-recursive root glob. So root README.md/CLAUDE.md/DEVELOPMENT.md are linted, but .pair/**/*.md (adoption + knowledge base), qa/**, docs/** and scripts/workflows/release/README.md are not.

Pre-existing (write mode had the same blind spot), but #394 made check coverage the whole value of the gate: the adoption/KB markdown edited by nearly every story in this repo is not covered by the check that is supposed to keep formatting out of unrelated diffs.

Likely In Scope

• Extend the root prettier:check/prettier:fix and mdlint:check/mdlint:fix scripts to cover non-workspace paths (root-level files, scripts/, .pair/, qa/, docs/) — check and fix must stay symmetric by construction
• Absorb the resulting one-time formatting sweep as its own commit (expect a large diff on .pair/**)
• Keep the .gitignore delegation working from the repo root cwd

Likely Out of Scope

• CI enforcement of format:check (see the companion story)
• Any write-mode formatter in the gate (banned — ADL 2026-07-31 + pnpm gate:composition)
• Changing markdownlint rules

Acceptance Criteria (draft)

• An unformatted .pair/**/*.md (or root-level JSON/TS) fails pnpm format:check
• pnpm format fixes exactly what pnpm format:check reports (same file set)
• Gitignored/generated trees stay excluded (no push blocked by generated output)

Notes

Filed from the independent review of PR #412, where it was raised twice as a Question and answered as "worth its own story". Sizing risk: the one-time sweep over .pair/** is the bulk of the work, not the script change.

[rucka]

Note from #412 (story #394) — the mirror-guard coupling belongs in this scope

The Problem section lists .claude/**/*.json as out of format scope, but not .claude/skills/**/*.md, and the omission has a consequence beyond "unchecked files": it makes the documented pnpm format remedy a two-step operation, or a trap.

Mechanism:

• packages/knowledge-hub/dataset/.skills/<cat>/<name>/SKILL.md is in format scope (it lives in a workspace package).
• Its generated twin .claude/skills/pair-<prefixed>/SKILL.md is not (.claude/ is not a workspace member; the root mdlint:check extra step globs a non-recursive `'*.md').
• packages/knowledge-hub/src/tools/skill-md-mirror.ts asserts the two are byte-equal, by regenerating the .claude copy from the dataset copy through the real pair update transform.

So a format-only edit to one side breaks the mirror guard, and skills:conformance runs later in the same gate than format:check. A contributor goes format:check-red → pnpm format → skills:conformance-red.

Reproduced for real while rebasing #412 onto current main: main carried 2x MD049 (*as of then*) at dataset/.skills/capability/assess-cost/SKILL.md:155. pnpm format rewrote it to _as of then_; the .claude twin still held the asterisk form, and skill-md-mirror.test.ts went red until the twin was propagated by hand.

Handled in #412 as documentation only — the two-step remedy is now stated in DEVELOPMENT.md, apps/website/content/docs/contributing/development-setup.mdx, and PRE_PUSH_REMEDY (with a unit test pinning it).

The structural fix is this story: bring both copies into ONE format scope, so pnpm format either reaches both or neither and the mirror guard cannot be broken by a formatter. Please add .claude/skills/**/*.md to the coverage list here, and treat "does not break skills:conformance" as an acceptance criterion of whatever scope widening this story lands.