Enhance LLM integration and improve documentation and functionality

.classpath

@@ -9,6 +9,7 @@
 	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="optional" value="true"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
@@ -18,7 +19,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-21">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
@@ -28,5 +29,26 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="test" value="true"/>
+			<attribute name="optional" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="target/generated-test-sources/test-annotations">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="test" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="ignore_optional_problems" value="true"/>
+			<attribute name="m2e-apt" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" path="target/generated-sources/annotations">
+		<attributes>
+			<attribute name="optional" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

.gitignore

@@ -2,6 +2,7 @@ target/
 ClassDiagram.png
 ClassDiagram.ucls
 Output/
+Output_temp/
 .classpath
 .project
 .settings/
@@ -10,4 +11,15 @@ Output/
 shippable/
 *.class
 *.temp
-dotFSMs/
+dotFSMs/
+*.env
+.venv/
+sanitized_rules/
+temp_rules/
+rag_cache/
+__pycache__/
+*.py[cod]
+llm/.venv/
+.settings/
+.run/
+.vscode/

.project

@@ -20,4 +20,15 @@
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 	</natures>
+	<filteredResources>
+		<filter>
+			<id>1745962974473</id>
+			<name></name>
+			<type>30</type>
+			<matcher>
+				<id>org.eclipse.core.resources.regexFilterMatcher</id>
+				<arguments>node_modules|\.git|__CREATED_BY_JAVA_LANGUAGE_SERVER__</arguments>
+			</matcher>
+		</filter>
+	</filteredResources>
 </projectDescription>

.run/CrySLDoc Generation.run.xml

@@ -0,0 +1,21 @@
+<component name="ProjectRunConfigurationManager">
+  <configuration default="false" name="CrySLDoc Generation" type="Application" factoryName="Application">
+    <option name="MAIN_CLASS_NAME" value="de.upb.docgen.DocumentGeneratorMain" />
+    <module name="DocGen" />
+    <option name="PROGRAM_PARAMETERS" value="--FTLtemplatesPath src/main/resources/FTLTemplates --reportPath Output --llm=on --llm-backend=openai" />
+    <option name="VM_PARAMETERS" value="-Dfile.encoding=UTF-8" />
+    <extension name="net.ashald.envfile">
+      <option name="IS_ENABLED" value="false" />
+      <option name="IS_SUBST" value="false" />
+      <option name="IS_PATH_MACRO_SUPPORTED" value="false" />
+      <option name="IS_IGNORE_MISSING_FILES" value="false" />
+      <option name="IS_ENABLE_EXPERIMENTAL_INTEGRATIONS" value="false" />
+      <ENTRIES>
+        <ENTRY IS_ENABLED="true" PARSER="runconfig" IS_EXECUTABLE="false" />
+      </ENTRIES>
+    </extension>
+    <method v="2">
+      <option name="Make" enabled="true" />
+    </method>
+  </configuration>
+</component>

.settings/org.eclipse.jdt.core.prefs

@@ -1,8 +1,20 @@
 eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
-org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.annotation.missingNonNullByDefaultAnnotation=ignore
+org.eclipse.jdt.core.compiler.annotation.nonnull=javax.annotation.Nonnull
+org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=javax.annotation.ParametersAreNonnullByDefault
+org.eclipse.jdt.core.compiler.annotation.nullable=javax.annotation.Nullable
+org.eclipse.jdt.core.compiler.annotation.nullanalysis=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=21
+org.eclipse.jdt.core.compiler.compliance=21
 org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.problem.nullAnnotationInferenceConflict=warning
+org.eclipse.jdt.core.compiler.problem.nullReference=warning
+org.eclipse.jdt.core.compiler.problem.nullSpecViolation=warning
+org.eclipse.jdt.core.compiler.problem.nullUncheckedConversion=ignore
+org.eclipse.jdt.core.compiler.problem.potentialNullReference=warning
 org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
-org.eclipse.jdt.core.compiler.release=disabled
-org.eclipse.jdt.core.compiler.source=1.8
+org.eclipse.jdt.core.compiler.problem.syntacticNullAnalysisForFields=enabled
+org.eclipse.jdt.core.compiler.processAnnotations=enabled
+org.eclipse.jdt.core.compiler.release=enabled
+org.eclipse.jdt.core.compiler.source=21

.vscode/settings.json

@@ -0,0 +1,6 @@
+{
+    "java.compile.nullAnalysis.mode": "automatic",
+    "python-envs.defaultEnvManager": "ms-python.python:conda",
+    "python-envs.defaultPackageManager": "ms-python.python:conda",
+    "python-envs.pythonProjects": []
+}