private void loadCompiledModules(
     List<JCCompilationUnit> trees, LinkedList<JCCompilationUnit> moduleTrees) {
   compilerDelegate.visitModules(phasedUnits);
   Modules modules = ceylonContext.getModules();
   // now make sure the phase units have their modules and packages set correctly
   for (PhasedUnit pu : phasedUnits.getPhasedUnits()) {
     Package pkg = pu.getPackage();
     loadModuleFromSource(pkg, modules, moduleTrees, trees);
   }
   // also make sure we have packages and modules set up for every Java file we compile
   for (JCCompilationUnit cu : trees) {
     // skip Ceylon CUs
     if (cu instanceof CeylonCompilationUnit) continue;
     String packageName = "";
     if (cu.pid != null) packageName = TreeInfo.fullName(cu.pid).toString();
     /*
      * Stef: see javadoc for findOrCreateModulelessPackage() for why this is here.
      */
     Package pkg = modelLoader.findOrCreateModulelessPackage(packageName);
     loadModuleFromSource(pkg, modules, moduleTrees, trees);
   }
   for (PhasedUnit phasedUnit : phasedUnits.getPhasedUnits()) {
     for (Tree.ModuleDescriptor modDescr :
         phasedUnit.getCompilationUnit().getModuleDescriptors()) {
       String name = phasedUnit.getPackage().getNameAsString();
       CeylonPhasedUnit cpu = (CeylonPhasedUnit) phasedUnit;
       CeylonFileObject cfo = (CeylonFileObject) cpu.getFileObject();
       moduleNamesToFileObjects.put(name, cfo);
     }
   }
 }
  private JCCompilationUnit ceylonParse(JavaFileObject filename, CharSequence readSource) {
    if (ceylonEnter.hasRun())
      throw new RuntimeException(
          "Trying to load new source file after CeylonEnter has been called: " + filename);
    try {
      ModuleManager moduleManager = phasedUnits.getModuleManager();
      File sourceFile = new File(filename.getName());
      // FIXME: temporary solution
      VirtualFile file = vfs.getFromFile(sourceFile);
      VirtualFile srcDir = vfs.getFromFile(getSrcDir(sourceFile));

      String source = readSource.toString();
      char[] chars = source.toCharArray();
      LineMap map = Position.makeLineMap(chars, chars.length, false);

      PhasedUnit phasedUnit = null;

      PhasedUnit externalPhasedUnit = compilerDelegate.getExternalSourcePhasedUnit(srcDir, file);

      if (externalPhasedUnit != null) {
        phasedUnit = new CeylonPhasedUnit(externalPhasedUnit, filename, map);
        phasedUnits.addPhasedUnit(externalPhasedUnit.getUnitFile(), phasedUnit);
        gen.setMap(map);

        String pkgName = phasedUnit.getPackage().getQualifiedNameString();
        if ("".equals(pkgName)) {
          pkgName = null;
        }
        return gen.makeJCCompilationUnitPlaceholder(
            phasedUnit.getCompilationUnit(), filename, pkgName, phasedUnit);
      }
      if (phasedUnit == null) {
        ANTLRStringStream input = new ANTLRStringStream(source);
        CeylonLexer lexer = new CeylonLexer(input);

        CommonTokenStream tokens = new CommonTokenStream(lexer);

        CeylonParser parser = new CeylonParser(tokens);
        CompilationUnit cu = parser.compilationUnit();

        java.util.List<LexError> lexerErrors = lexer.getErrors();
        for (LexError le : lexerErrors) {
          printError(le, le.getMessage(), "ceylon.lexer", map);
        }

        java.util.List<ParseError> parserErrors = parser.getErrors();
        for (ParseError pe : parserErrors) {
          printError(pe, pe.getMessage(), "ceylon.parser", map);
        }

        if (lexerErrors.size() == 0 && parserErrors.size() == 0) {
          // FIXME: this is bad in many ways
          String pkgName = getPackage(filename);
          // make a Package with no module yet, we will resolve them later
          /*
           * Stef: see javadoc for findOrCreateModulelessPackage() for why this is here.
           */
          com.redhat.ceylon.compiler.typechecker.model.Package p =
              modelLoader.findOrCreateModulelessPackage(pkgName == null ? "" : pkgName);
          phasedUnit =
              new CeylonPhasedUnit(
                  file, srcDir, cu, p, moduleManager, ceylonContext, filename, map);
          phasedUnits.addPhasedUnit(file, phasedUnit);
          gen.setMap(map);

          return gen.makeJCCompilationUnitPlaceholder(cu, filename, pkgName, phasedUnit);
        }
      }
    } catch (RuntimeException e) {
      throw e;
    } catch (Exception e) {
      throw new RuntimeException(e);
    }

    JCCompilationUnit result =
        make.TopLevel(List.<JCAnnotation>nil(), null, List.<JCTree>of(make.Erroneous()));
    result.sourcefile = filename;
    return result;
  }