Close to good solution. Just need to confirm .java file updates.

java/src/processing/mode/java/ErrorChecker.java

@@ -89,7 +89,7 @@ class ErrorChecker {
     if (ps.compilationUnit == null) {
       iproblems = new IProblem[0];
     } else {
-      iproblems = ps.compilationUnit.getProblems();
+      iproblems = ps.iproblems;
     }
 
     final List<Problem> problems = new ArrayList<>(ps.otherProblems);
@@ -117,6 +117,8 @@ class ErrorChecker {
           // See: https://bugs.eclipse.org/bugs/show_bug.cgi?id=405780
           .filter(iproblem -> !iproblem.getMessage()
               .contains("Syntax error, insert \":: IdentifierOrNew\""))
+          .filter(iproblem -> !iproblem.getMessage()
+              .contains("must be defined in its own file"))
           // Transform into our Problems
           .map(iproblem -> {
             JavaProblem p = convertIProblem(iproblem, ps);

java/src/processing/mode/java/PreprocService.java

@@ -353,7 +353,7 @@ public class PreprocService {
     // Combine code into one buffer
     int numLines = 1;
     IntList tabStartsList = new IntList();
-    List<SketchCode> javaFiles = new ArrayList<>();
+    List<JavaSketchCode> javaFiles = new ArrayList<>();
     List<Integer> tabLineStarts = new ArrayList<>();
     for (SketchCode sc : sketch.getCode()) {
       if (sc.isExtension("pde")) {
@@ -376,7 +376,14 @@ public class PreprocService {
         numLines += SourceUtil.getCount(newPieceBuilt, "\n");
         workBuffer.append(newPieceBuilt);
       } else if (sc.isExtension("java")) {
-        javaFiles.add(sc);
+        tabStartsList.append(workBuffer.length());
+        tabLineStarts.add(numLines);
+
+        javaFiles.add(new JavaSketchCode(sc, tabStartsList.size()-1));
+
+        String newPieceBuilt = "\n//Skip java file\n";
+        numLines += SourceUtil.getCount(newPieceBuilt, "\n");
+        workBuffer.append(newPieceBuilt);
       }
     }
     result.tabStartOffsets = tabStartsList.array();
@@ -500,15 +507,15 @@ public class PreprocService {
 
     // Generate bindings after getting problems - avoids
     // 'missing type' errors when there are syntax problems
-    CompilationUnit bindingsCU;
+    FinalCompileResults finalCompile;
     if (javaFiles.size() == 0) {
-      bindingsCU = compileInMemory(
+      finalCompile = compileInMemory(
           compilableStage,
           className,
           result.classPathArray
       );
     } else {
-      bindingsCU = compileFromDisk(
+      finalCompile = compileFromDisk(
           compilableStage,
           className,
           result.classPathArray,
@@ -517,14 +524,16 @@ public class PreprocService {
     }
 
     // Get compilation problems
-    List<IProblem> bindingsProblems = Arrays.asList(bindingsCU.getProblems());
+    List<IProblem> bindingsProblems = finalCompile.getProblems();
     result.hasCompilationErrors =
       bindingsProblems.stream().anyMatch(IProblem::isError);
 
     // Update builder
     result.offsetMapper = parsableMapper.thenMapping(compilableMapper);
     result.javaCode = compilableStage;
-    result.compilationUnit = bindingsCU;
+    result.compilationUnit = finalCompile.getCompilationUnit();
+    result.javaFileMapping = finalCompile.getJavaFileMapping();
+    result.iproblems = finalCompile.getProblems();
 
     // Build it
     return result.build();
@@ -532,7 +541,7 @@ public class PreprocService {
 
   /// FINAL COMPILATION -------------------------------------------------------
 
-  private CompilationUnit compileInMemory(String compilableStage,
+  private FinalCompileResults compileInMemory(String compilableStage,
       String className, String[] classPathArray) {
 
     parser.setSource(compilableStage.toCharArray());
@@ -542,13 +551,18 @@ public class PreprocService {
     parser.setUnitName(className);
     parser.setEnvironment(classPathArray, null, null, false);
     parser.setResolveBindings(true);
-    return (CompilationUnit) parser.createAST(null);
+
+    CompilationUnit compilationUnit = (CompilationUnit) parser.createAST(null);
+    List<IProblem> problems = Arrays.asList(compilationUnit.getProblems());
+    return new FinalCompileResults(compilationUnit, problems, new HashMap<>());
   }
 
-  private CompilationUnit compileFromDisk(String compilableStage,
-      String className, String[] classPathArray, List<SketchCode> javaFiles) {
+  private FinalCompileResults compileFromDisk(String compilableStage,
+      String className, String[] classPathArray,
+      List<JavaSketchCode> javaFiles) {
 
     List<Path> temporaryFilesList = new ArrayList<>();
+    Map<String, Integer> javaFileMapping = new HashMap<>();
 
     // Prepare preprocessor
     parser.setKind(ASTParser.K_COMPILATION_UNIT);
@@ -564,8 +578,9 @@ public class PreprocService {
     temporaryFilesList.add(mainTemporaryFile);
 
     // Write temporary java files
-    for (SketchCode javaFile : javaFiles) {
-      Path newPath = createTemporaryFile(javaFile.getProgram());
+    for (JavaSketchCode javaFile : javaFiles) {
+      Path newPath = createTemporaryFile(javaFile.getSketchCode().getProgram());
+      javaFileMapping.put(newPath.toString(), javaFile.getTabIndex());
       temporaryFilesList.add(newPath);
     }
 
@@ -577,7 +592,8 @@ public class PreprocService {
     }
 
     // Compile
-    MutableCompiledUnit compiledHolder = new MutableCompiledUnit();;
+    final MutableCompiledUnit compiledHolder = new MutableCompiledUnit();
+    final List<IProblem> problems = new ArrayList<>();
     parser.createASTs(
         temporaryFilesArray,
         null,
@@ -587,6 +603,12 @@ public class PreprocService {
             if (source.equals(mainSource)) {
               compiledHolder.set(ast);
             }
+
+            for (IProblem problem : ast.getProblems()) {
+              System.out.println("Found problem in " + source);
+              System.out.println(problem);
+              problems.add(problem);
+            }
           }
         },
         null
@@ -596,7 +618,11 @@ public class PreprocService {
     deleteFiles(temporaryFilesList);
 
     // Return
-    return compiledHolder.get();
+    return new FinalCompileResults(
+        compiledHolder.get(),
+        problems,
+        javaFileMapping
+    );
   }
 
   private Path createTemporaryFile(String content) {
@@ -631,6 +657,51 @@ public class PreprocService {
     }
   }
 
+  private class FinalCompileResults {
+    private final CompilationUnit compilationUnit;
+    private final List<IProblem> problems;
+    private final Map<String, Integer> javaFileMapping;
+
+    public FinalCompileResults(CompilationUnit newCompilationUnit,
+        List<IProblem> newProblems, Map<String, Integer> newJavaFileMapping) {
+
+      compilationUnit = newCompilationUnit;
+      problems = newProblems;
+      javaFileMapping = newJavaFileMapping;
+    }
+
+    public CompilationUnit getCompilationUnit() {
+      return compilationUnit;
+    }
+
+    public List<IProblem> getProblems() {
+      return problems;
+    }
+
+    public Map<String, Integer> getJavaFileMapping() {
+      return javaFileMapping;
+    }
+  }
+
+  private class JavaSketchCode {
+    private SketchCode sketchCode;
+    private int tabIndex;
+
+    public JavaSketchCode(SketchCode newSketchCode, int newTabIndex) {
+      sketchCode = newSketchCode;
+      tabIndex = newTabIndex;
+    }
+
+    public SketchCode getSketchCode() {
+      return sketchCode;
+    }
+
+    public int getTabIndex() {
+      return tabIndex;
+    }
+
+  }
+
   /// IMPORTS -----------------------------------------------------------------
 
   private List<ImportStatement> coreAndDefaultImports;

java/src/processing/mode/java/PreprocSketch.java

@@ -11,6 +11,7 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 
 import processing.app.Problem;
 import processing.app.Sketch;
@@ -44,6 +45,9 @@ public class PreprocSketch {
   public final List<ImportStatement> coreAndDefaultImports;
   public final List<ImportStatement> codeFolderImports;
   public final List<Problem> otherProblems;
+  public final List<IProblems> iproblems;
+
+  public final Map<String, Integer> javaFileMapping;
 
   /// JAVA -> SKETCH -----------------------------------------------------------
 
@@ -69,8 +73,27 @@ public class PreprocSketch {
 
 
   public SketchInterval mapJavaToSketch(IProblem iproblem) {
-    return mapJavaToSketch(iproblem.getSourceStart(),
-                           iproblem.getSourceEnd() + 1); // make it exclusive
+    String originalFile = new String(iproblem.getOriginatingFileName());
+    System.out.println("here!!");
+    System.out.println(originalFile);
+    System.out.println(javaFileMapping.keySet());
+    System.out.println(iproblem);
+    boolean isJavaFile = javaFileMapping.containsKey(originalFile);
+
+    if (isJavaFile) {
+      return new SketchInterval(
+          javaFileMapping.get(originalFile),
+          iproblem.getSourceStart(),
+          iproblem.getSourceEnd() + 1,
+          -1, // Is outside sketch code
+          -1  // Is outside sketch code
+      );
+    } else {
+      return mapJavaToSketch(
+          iproblem.getSourceStart(),
+          iproblem.getSourceEnd() + 1  // make it exclusive
+      );
+    }
   }
 
 
@@ -213,6 +236,9 @@ public class PreprocSketch {
     public final List<ImportStatement> coreAndDefaultImports = new ArrayList<>();
     public final List<ImportStatement> codeFolderImports = new ArrayList<>();
     public final List<Problem> otherProblems = new ArrayList<>();
+    public List<IProblems> iproblems;
+
+    public Map<String, Integer> javaFileMapping;
 
     public PreprocSketch build() {
       return new PreprocSketch(this);
@@ -247,6 +273,9 @@ public class PreprocSketch {
 
     otherProblems = b.otherProblems;
 
+    javaFileMapping = b.javaFileMapping;
+    iproblems = b.iproblems;
+
     programImports = Collections.unmodifiableList(b.programImports);
     coreAndDefaultImports = Collections.unmodifiableList(b.coreAndDefaultImports);
     codeFolderImports = Collections.unmodifiableList(b.codeFolderImports);