fix major bug and improve model integrity detection

this commit will likely hurt performance by a lot, because previous optimizations had to be removed in the Evaluator

autograder-core/src/main/java/de/firemage/autograder/core/CodeModel.java

@@ -11,12 +11,18 @@
 import spoon.processing.AbstractProcessor;
 import spoon.processing.Processor;
 import spoon.reflect.CtModel;
+import spoon.reflect.code.CtCatchVariable;
 import spoon.reflect.code.CtTargetedExpression;
 import spoon.reflect.declaration.*;
+import spoon.reflect.factory.CodeFactory;
 import spoon.reflect.factory.Factory;
+import spoon.reflect.factory.FactoryImpl;
+import spoon.reflect.reference.CtCatchVariableReference;
 import spoon.reflect.reference.CtReference;
 import spoon.reflect.visitor.*;
 import spoon.reflect.visitor.filter.NamedElementFilter;
+import spoon.support.DefaultCoreFactory;
+import spoon.support.StandardEnvironment;
 
 import java.io.IOException;
 import java.net.MalformedURLException;
@@ -139,7 +145,36 @@ private void buildModelMaybe() {
                 return;
             }
 
-            Launcher launcher = new Launcher();
+
+            // Fix for something similar to https://github.com/INRIA/spoon/issues/5868
+            Factory baseFactory = new FactoryImpl(new DefaultCoreFactory(), new StandardEnvironment()) {
+                private transient CodeFactory code;
+
+                @Override
+                public CodeFactory Code() {
+                    if (this.code == null) {
+                        this.code = new CodeFactory(this) {
+                            @Override
+                            public <T> CtCatchVariableReference<T> createCatchVariableReference(CtCatchVariable<T> catchVariable) {
+                                // The implementation of the original method is broken, resulting in elements which point to the
+                                // wrong or an invalid parent.
+                                //
+                                // This is a workaround until the issue is fixed in spoon.
+                                CtCatchVariableReference<T> ref = this.factory.Core().createCatchVariableReference();
+
+                                ref.setType(catchVariable.getType() == null ? null : catchVariable.getType().clone());
+                                ref.setSimpleName(catchVariable.getSimpleName());
+                                ref.setParent(catchVariable);
+
+                                return ref;
+                            }
+                        };
+                    }
+                    return this.code;
+                }
+            };
+
+            Launcher launcher = new Launcher(baseFactory);
             launcher.addInputResource(file.getSpoonResource());
             launcher.getEnvironment().setShouldCompile(false);
             launcher.getEnvironment().setSourceClasspath(new String[]{jar.toAbsolutePath().toString()});

autograder-core/src/main/java/de/firemage/autograder/core/Linter.java

@@ -187,11 +187,9 @@ public List<Problem> checkFile(
 
         AnalysisResult result;
         try (TempLocation tempLinterLocation = this.tempLocation.createTempDirectory("linter")) {
-            Path tmpLocation = tempLinterLocation.toPath();
-
             if (!integratedChecks.isEmpty()) {
                 scheduler.submitTask((s, reporter) -> {
-                    IntegratedAnalysis analysis = new IntegratedAnalysis(file, tmpLocation);
+                    IntegratedAnalysis analysis = new IntegratedAnalysis(file);
                     analysis.lint(integratedChecks, statusConsumer, s);
                 });
             }

autograder-core/src/main/java/de/firemage/autograder/core/check/exceptions/ExceptionMessageCheck.java

@@ -24,7 +24,8 @@ private static boolean isExceptionWithoutMessage(CtExpression<?> expression) {
             return false;
         }
 
-        // check if the invoked constructor passes a message to the exception
+        // check if the invoked constructor passes a message to the parent exception like this:
+        // class MyException extends Exception { MyException() { super("here is the message"); } }
         if (ctConstructorCall.getExecutable().getExecutableDeclaration() instanceof CtConstructor<?> ctConstructor
             && ctConstructor.getBody().filterChildren(ctElement -> ctElement instanceof CtInvocation<?> ctInvocation
                 // we just check if there is any invocation with a message, because this is easier and might be enough

autograder-core/src/main/java/de/firemage/autograder/core/file/UploadedFile.java

@@ -16,17 +16,29 @@
 import java.util.Optional;
 import java.util.function.Consumer;
 
-public class UploadedFile implements AutoCloseable {
+public final class UploadedFile implements AutoCloseable {
     private static final Logger LOG = LoggerFactory.getLogger(UploadedFile.class);
 
     private final CodeModel model;
     private final SourceInfo source;
     private final CompilationResult compilationResult;
+    private final ClassLoader classLoader;
+    private final TempLocation tempLocation;
 
-    private UploadedFile(CodeModel model, SourceInfo source, CompilationResult compilationResult) {
+    private UploadedFile(CodeModel model, SourceInfo source, CompilationResult compilationResult, ClassLoader classLoader, TempLocation tempLocation) {
         this.model = model;
         this.source = source;
         this.compilationResult = compilationResult;
+        this.classLoader = classLoader;
+        this.tempLocation = tempLocation;
+    }
+
+    public UploadedFile copy() {
+        try {
+            return UploadedFile.build(this.source, this.tempLocation.createTempDirectory("copy"), unused -> {}, this.classLoader);
+        } catch (IOException | CompilationFailureException exception) {
+            throw new IllegalStateException(exception);
+        }
     }
 
     public static UploadedFile build(
@@ -54,7 +66,7 @@ public static UploadedFile build(
 
         var model = CodeModel.buildFor(source, compilationResult.get().jar(), classLoader);
 
-        return new UploadedFile(model, source, compilationResult.get());
+        return new UploadedFile(model, source, compilationResult.get(), classLoader, tmpLocation);
     }
 
     public SourceInfo getSource() {