Fixed runtime configuration

- Timeout overrides retain original values for restoration
- Timeout restoration preserves operator changes and symbolic links
- Tests cover timeout persistence and failed configuration writes
- Runtime targets use separate Gradle caches and shared module outputs
- Modded build inputs include test fixtures and runtime cache settings

settings.gradle

@@ -22,6 +22,7 @@ plugins {
 
 rootProject.name = 'Iris'
 
+apply from: new File(settingsDir, 'gradle/runtime-cache.settings.gradle')
 apply from: new File(settingsDir, 'gradle/volmlib-resolution.settings.gradle')
 
 include(':core', ':core:agent')