Docs: describe the --sync-bodies exception to the direction contract #9

Deferred from #7 (decision 3). The README's and CLAUDE.md's contract tables state a clean bidirectional rule — populate: file → GitHub at bootstrap; update: GitHub → file thereafter — and `populate --sync-bodies` is now a deliberate exception: file → GitHub for issue BODIES and milestone DESCRIPTIONS of already-existing items, on explicit request only, with refuse-on-divergence semantics (`--force` = last writer wins).

The concern: the contract tables are the template's core teaching device, and exceptions listed casually erode them. The docs need a formulation that keeps the tables crisp while stating precisely when the exception applies (explicit flag, existing items only, never run by workflows) and what protects GitHub-side edits (per-item divergence refusal; the engine stores no base version).