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migrate_to_0_3_1 no longer deletes a project's own <umbrella>/scripts/. The 0.3.1 migration detected the pre-0.3.1 flat engine by the bare presence of <umbrella>/scripts/ and then rm -rf'd it — but a modular project may legitimately keep its own tooling there (build/design scripts, tests, fixtures), and the migration relocated the real engine into sync/ while deleting the project's code as "legacy". Because run_migrations walks the whole chain on every update.sh, this fired on each update, not once. The flat engine is now identified by its entry script scripts/sync.sh — the same sentinel the migration's own postcondition already verifies — so a <umbrella>/scripts/ without it is left untouched, and the destructive cleanup is guarded by the same sentinel. A genuine pre-0.3.1 layout (which always ships scripts/sync.sh) still migrates exactly as before; a modular project that owns <umbrella>/scripts/ is now a correct no-op. No schema change — the stamp advances to 0.7.3 on update; re-run sync afterwards.