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>

scripts/verify/rea-numeric-limits.mjs

@@ -857,20 +857,11 @@ export const parseRuntimeSettingEnvironments = (source) => {
   return names;
 };
 
-/** Existing launch-seed migrations. A new per-call policy is rejected. */
-const TEMPORARY_PER_CALL_LIMITS = new Set([
-  "REA_BRIDGE_MAX_REQUEST_BYTES",
-  "REA_DEBUGGER_COMMAND_DEADLINE_MS",
-  "REA_DEBUGGER_MAX_COMMAND_OUTPUT_BYTES",
-  "REA_HOPPER_CALLER_SCAN_BUDGET_MS",
-  "REA_JEB_MCP_TIMEOUT_MS",
-  "REA_KUNA_PROJECT_TIMEOUT_MS",
-  "REA_KUNA_TIMEOUT_MS",
-  "REA_PWNTOOLS_MAX_INPUT_BYTES",
-  "REA_WINDOWS_CHANGE_TIME_DRIFT_MS",
-  "REA_WINDOWS_CHANGE_TIME_SETTLE_MAX_POLLS",
-  "REA_WINDOWS_CHANGE_TIME_SETTLE_POLL_MS",
-]);
+/**
+ * Names still registered as per-call while they move into ANALYSIS_SETTINGS.
+ * This branch has moved those limits, so the allowlist is empty.
+ */
+const TEMPORARY_PER_CALL_LIMITS = new Set([]);
 
 /** Temporary exceptions must be removed from both the registry and allowlist. */
 export const perCallLimitFailures = (listed, temporary) => {
@@ -908,15 +899,7 @@ if (direct) {
       failures.push(
         `${name} is both a runtime setting and on the exception list`,
       );
-    if (policy === "restart-only" && read === "per-call")
-      failures.push(
-        `${name} is restart-only but is recorded as a per-call read`,
-      );
-    if (
-      policy === "restart-only" &&
-      read !== "startup" &&
-      read !== "construction"
-    )
+    if (read !== "startup" && read !== "construction")
       failures.push(`${name} is restart-only but is not read at startup`);
   }
   failures.push(
@@ -1055,7 +1038,7 @@ if (direct) {
     process.exit(1);
   }
   console.log(
-    `Numeric REA_ limits: ${runtime.size} runtime, ${[...listed.values()].filter((entry) => entry.policy === "restart-only").length} restart-only, ${[...listed.values()].filter((entry) => entry.policy === "per-call").length} per-call pending migration, ${discovered.size} discovered.`,
+    `Numeric REA_ limits: ${runtime.size} runtime, ${listed.size} restart-only, ${discovered.size} discovered.`,
   );
   console.log(
     "Read-site kinds describe syntax only; Node lint does not verify reachability, invocation frequency or complete reader coverage.",