bos upgrade re-clobbers child-restored root package.json scripts — default test script also silently exits 1 on repos without plugins/

Start by tracing the bos upgrade reconciliation source that writes the root package.json scripts, then compare its test and typecheck loops and the v2.0.0-rc.27 template. Reproduce with a child repo that has no plugins/ directory and custom packages/* scripts. Done means upgrades preserve or clearly report child edits, and the default test script succeeds without plugins while retaining package coverage.

bos upgrade resets child-restored root package.json scripts — and its reconcile source's default test script silently exits 1 on repos without plugins/

Child evidence (activity.nearbuilders.org, v2.0.0-rc.27)

Two separate defects, both observed on the managed v1→v2 upgrade branch (#82, merged as NEARBuilders/activity.nearbuilders.org#82 / #89):

1. Upgrade reconcile overwrites child customizations in root scripts

C1 restored packages/* coverage in the root scripts (the child publishes @nearbuilders/activity-client from packages/client):

test:      … pnpm --dir ui … run test && for dir in packages/*; do if [ -f "$dir/package.json" ]; then pnpm --dir "$dir" --if-present run test || exit 1; fi; done
typecheck: … pnpm --dir ui … && pnpm --dir api … && for dir in packages/*; do if [ -f "$dir/package.json" ]; then pnpm --dir "$dir" --if-present run typecheck || exit 1; fi; done

A later bos upgrade (rc.24 → rc.27, commit ac3ff53) reset both scripts to the framework reconcile versions:

test:      … && for d in plugins/*; do [ -f "$d/package.json" ] && pnpm --dir "$d" --if-present run test; done
typecheck: … if [ -d plugins ]; then for dir in plugins/*; do …; fi; fi

• packages/* coverage was silently dropped from both the test and typecheck gates.
• The test reset made CI go red: the repo has no plugins/ directory, the glob stays literal, [ -f "plugins/*/package.json" ] returns false → the unguarded && chain is the last command → the script exits 1 with zero output (the Test job failed 56 ms after the UI suite passed, no failing test to find).

.bos/sync-backup/2026-10-29T04-17-…/package.json did capture the pre-upgrade copy (good), but nothing surfaced that the child's customizations were being reset — the red CI was how we found out. The child re-restored the scripts in NEARBuilders/activity.nearbuilders.org#89's parent commit (909c2b2) and this has now happened twice in the same migration (restored, re-clobbered, re-restored).

2. The reconcile source's default test script fails for plugin-less children

The reset version differs from the upstream template (v2.0.0-rc.27 template root test is pnpm run test:ui && test:api && test:e2e && test:framework), so the plugins/* loop comes from the upgrade's reconcile source — and it has a robustness bug the typecheck sibling doesn't share: typecheck guards with if [ -d plugins ], the test loop is unguarded. Any child without plugins/ would get a silently red test script from the framework's own machinery.

Expected behavior

• bos upgrade reconciliation should patch rather than reset child-modified sections of files it reconciles (or, minimally, report exactly which child customizations were dropped, not just create a .bos/sync-backup copy). Related but distinct: #650 (v1→v1 one-shot drops) and #659 (stale overrides shadowing the catalog — that one's the same upgrade run pointing the #546 skew gate at the wrong fix).
• The framework's default root test script should be exit-0-safe for repos without plugins/ (same guard as typecheck), and ideally include a packages/* loop (or generate one from workspace globs) so published children keep their test/typecheck coverage after upgrades.

Repro

1. Child repo: everything-dev v2 app, restore packages/* loops in root test/typecheck (or any repo with no plugins/ dir).
2. Run bos upgrade to a newer rc.
3. Root scripts are reset to the plugins/* variants; pnpm run test now exits 1 silently after the ui suite finishes (see NEARBuilders/activity.nearbuilders.org CI run 40817136914, CI / Test: api 155 ✓, ui 109 ✓, then ELIFECYCLE Test failed).

Child fix commits for reference: 909c2b2 (re-restore) and 96c3be5/44b40a5 (#89, overrides realignment also surfaced by the same upgrade run).