gradle warnings, integrate review comments from BenjaminAmos

cherry picked PurityLakes pr #5140
onto newest develop. kotlin plugin and spotbugs conflict comments are resolved
by this.

protobuf upgrade should be compabitle, at least according to documentation, so
left it there.

the lenient in module_deps.kt is again there:
```
val artifactView = resolvable.artifactView {
  lenient(true)
}
```

build-logic/src/main/kotlin/org/terasology/gradology/module_deps.kt

@@ -90,6 +90,9 @@ fun moduleDependencyOrdering(modulesConfig: Configuration): List<String> {
     // configurations.resolvedConfiguration is more straightforward if you just want all the artifacts,
     // but using `.incoming` lets us turn on lenient mode as well as do more accurate filtering of local modules
     val resolvable = modulesConfig.incoming
+    val artifactView = resolvable.artifactView {
+        lenient(true)
+    }
 
     val result = resolvable.resolutionResult
     val allDependencies = result.allDependencies