import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
import java.util.Collections;
import java.util.ArrayList;
import javax.annotation.processing.*;
import javax.lang.model.*;
import javax.lang.model.element.Element;
import javax.lang.model.element.TypeElement;
import javax.lang.model.element.ElementKind;
import javax.tools.*;
import com.sun.source.util.Trees;
import com.sun.source.util.TreePath;
import com.sun.tools.javac.processing.JavacProcessingEnvironment;
import com.sun.tools.javac.tree.*;
import com.sun.tools.javac.util.*;
import com.sun.tools.javac.tree.JCTree.*;
import com.sun.tools.javac.util.List;
import com.sun.tools.javac.util.Name;
import com.sun.tools.javac.model.JavacElements;
import javax.lang.model.util.Elements;

@SupportedAnnotationTypes("*")
@SupportedOptions("replaces")
@SupportedSourceVersion(SourceVersion.RELEASE_7)
public class ReplaceMixer extends AbstractProcessor {
	private Trees trees;
	private TreeMaker make;
	private JavacElements elements;

	private HashMap<String, JCTree> cleanMethods = new HashMap<>();
	private HashMap<String, JCTree> cleanInnerClasses = new HashMap<>();
	private HashMap<String, JCTree> cleanFields = new HashMap<>();
	private boolean isPublic = true;
	private boolean imported = false;
	private boolean isCleanroom;
	private int classLevel;

	public String[] replaces = null;

	@Override
	public synchronized void init(ProcessingEnvironment env) {
		super.init(env);
		trees = Trees.instance(env);
		Context context = ((JavacProcessingEnvironment) env).getContext();
		make = TreeMaker.instance(context);
		elements = JavacElements.instance(context);
		String repString = env.getOptions().get("replaces");
		if (repString != null) {
			replaces = repString.split("#");
		}
	}

	@Override
	public boolean process(Set<? extends TypeElement> annotations, RoundEnvironment roundEnv) {
		if (!roundEnv.processingOver()) {
			Set<? extends Element> elements = roundEnv.getRootElements();
			for (Element each : elements) {
				Element encl = each.getEnclosingElement();
				if (encl != null) {
					// check if inside package cleanroom
					isCleanroom = encl.getSimpleName().toString().equals("cleanroom");
				} else {
					isCleanroom = false;
				}
				if (each.getKind() == ElementKind.CLASS) {
					classLevel = 0;
					JCTree tree = (JCTree) trees.getTree(each);
					tree.accept(new Merger());

					TreePath path = trees.getPath(each);

					if (!imported) { 
						imported = true;
						java.util.List imports = path.getCompilationUnit().getImports();
						for (Object o : imports) {
							System.out.println(o);
						}
					}

					if (!isCleanroom) {
						System.out.println(tree);
						// even with -proc:only the javac does some semantic checking
						// to avoid that (we compile the generated files anyway in the next step), exit in a clean way
						System.exit(0);
					}
				}
			}
		}
		return false;
	}

	private boolean isReplace(String method) {
		if (replaces == null) return false;
		for (String s : replaces) {
			if (method.startsWith(s)) return true;
		}
		return false;
	}

	private class Merger extends TreeTranslator {
		public boolean insideBlock = false;

		@Override
		public void visitBlock(JCBlock tree) {
			insideBlock = true;
			super.visitBlock(tree);
			insideBlock = false;
		}

		@Override
		public void visitVarDef(JCVariableDecl tree) {
			super.visitVarDef(tree);

			if (insideBlock) return;

			String name = tree.name.toString();
			if (isCleanroom && name.startsWith("__clean")) {
				cleanFields.put(name, tree);
			}
		}

		@Override
		public void visitMethodDef(JCMethodDecl tree) {
			super.visitMethodDef(tree);

			if (classLevel != 1) return;
			if (!isPublic) return;

			ArrayList<String> types = new ArrayList<>();
			for (JCVariableDecl decl : tree.params) {
				types.add(decl.vartype.toString());
			}
			String name = tree.name.toString() + ": " +  Arrays.toString(types.toArray());
			if (isCleanroom) {
				cleanMethods.put(name, tree);
			} else {
				if (cleanMethods.get(name) != null) {
					if (isReplace(name)) {
						System.err.println("duplicate method: " + name + ", taken from cleanroom");
						result = cleanMethods.get(name);
					} else {
						System.err.println("duplicate method: " + name + ", taken from student");
					}
					// we use that method, so don't put it in later in
					cleanMethods.remove(name);
				}
			}
		}

		private List<JCTree> appendAll(List<JCTree> list, Map<String, JCTree> cleanObjects) {
			for (Map.Entry<String, JCTree> entry : cleanObjects.entrySet()) {
				list = list.append(entry.getValue());
			}
			return list;
		}

		@Override
		public void visitClassDef(JCClassDecl tree) {
			JCModifiers mods = tree.getModifiers();
			boolean oldPublic = isPublic;
			isPublic = mods.getFlags().contains(javax.lang.model.element.Modifier.PUBLIC);
			System.err.println("class " + tree.name + " ispub " + isPublic);
			insideBlock = false;
			classLevel++;
			if (classLevel > 1) {
				System.err.println("found inner class: " + tree.name);
			}
			super.visitClassDef(tree);
			classLevel--;
			isPublic = oldPublic;

			System.err.println("class " + tree.name + ", " + isCleanroom + ", " + classLevel + ", " + isPublic);

			if (isCleanroom && classLevel >= 1 && tree.name.toString().startsWith("__clean")) {
				// remember additional inner classes of cleanroom
				// those will be added later in student's public class
				cleanInnerClasses.put(tree.name.toString(), tree);
			}

			// only add methods, fields and inner classes in
			// outer
			// public class
			// of student
			if (classLevel >= 1) return; // no outer class
			if (!mods.getFlags().contains(javax.lang.model.element.Modifier.PUBLIC)) return; // no public class
			if (isCleanroom) return; // no student class

			tree.defs = appendAll(tree.defs, cleanMethods);
			tree.defs = appendAll(tree.defs, cleanFields);
			tree.defs = appendAll(tree.defs, cleanInnerClasses);
			
			result = tree;
		}
	}
}

@@ -967,16 +967,63 @@
 essor %7B%0A
+%09public final String CLEAN_PREFIX = %22__clean%22;%0A
 %09private
@@ -3591,33 +3591,36 @@
 .startsWith(
-%22__clean%22
+CLEAN_PREFIX
 )) %7B%0A%09%09%09%09cle
@@ -5384,25 +5384,28 @@
 rtsWith(
-%22__clean%22
+CLEAN_PREFIX
 )) %7B%0A%09%09%09

Reduce string duplication.