A budget stop that kept its partial output exits 1 in atoms, probe, routing and analyze; tools preference exits 3 #632

The issue asks that a --max-usd stop that kept its partial output exit 3, as tools preference does (the exit-code table in docs/quickstart.md says only that command does, and "other commands still exit 1"). atoms, probe, routing and now analyze (commands/novelty_budget.py exit_partial, SystemExit(message)) exit 1, and tests pin that.

Changing them together reverses documented behaviour and the tests that pin it, and an open PR is already moving the exit codes. Fix: one decision on the exit code for a kept partial result, then change exit_partial and the routing exit in one place, with the doc table and tests.

Found while fixing #624. The fix's PR is #633.