refactor: adopt pkg/atomicfile for hand-rolled temp-file+rename writes

## Summary
Hand-rolled temp-file+rename atomic writes exist in 4 places while `pkg/atomicfile` already exists and is used by 9 other packages:
- `pkg/gateway/catalog.go:199-245`
- `pkg/cache/cache.go:341`
- `pkg/board/git.go:82`
- `pkg/runregistry/registry.go:101`

## Fix
Consolidate these onto `pkg/atomicfile`.

## Acceptance
- All four sites use pkg/atomicfile; behavior preserved; tests green.