fix(settings): preserve runtime contracts while restacking operation limits

Retain the original stack merge resolutions for runtime update modes, migrated guard exceptions, deadline ownership and boundary expectations on the merged settings base.

Co-authored-by: gensokyo-dev <342580529+gensokyo-dev@users.noreply.github.com>

src/application/AnalysisSettings.test.ts

@@ -291,8 +291,7 @@ it("rejects an out-of-range per-call limit and reads an accepted value from the
   expect(accepted.ok).toBe(true);
   if (!accepted.ok) return;
   expect(accepted.value).toMatchObject({
-    effect: "immediate",
-    rea_restart_required: false,
+    pending_restart: false,
   });
   const parsed = parseConfig({});
   if (!parsed.ok) throw parsed.error;