diff --git a/app/src/processing/app/Sketch.java b/app/src/processing/app/Sketch.java
index 1d540c3741c..f87286209ed 100644
--- a/app/src/processing/app/Sketch.java
+++ b/app/src/processing/app/Sketch.java
@@ -678,6 +678,10 @@ public void setModified(boolean state) {
     //new Exception().printStackTrace();
     current.setModified(state);
     calcModified();
+    // Remove any status notice, fx. done saving or done uploading,
+    // to avoid confusion about if the current code is the version
+    //in the board or not while debugging.
+    editor.statusNotice("");
   }
 
 
diff --git a/app/src/processing/app/preproc/PdePreprocessor.java b/app/src/processing/app/preproc/PdePreprocessor.java
index 2b4f03e85a6..e15f1087081 100644
--- a/app/src/processing/app/preproc/PdePreprocessor.java
+++ b/app/src/processing/app/preproc/PdePreprocessor.java
@@ -43,14 +43,14 @@ Processing version Copyright (c) 2004-05 Ben Fry and Casey Reas
  */
 public class PdePreprocessor {
   // stores number of built user-defined function prototypes
-  public int prototypeCount = 0;
+  public int generatedPrototypeCount = 0;
 
   // stores number of included library headers written
   // we always write one header: Arduino.h
   public int headerCount = 1;
   
   // the prototypes that are generated by the preprocessor
-  List<String> prototypes;
+  List<String> generatedPrototypes;
 
   // these ones have the .* at the end, since a class name might be at the end
   // instead of .* which would make trouble other classes using this can lop
@@ -126,10 +126,10 @@ public int writePrefix(String program, String buildPath,
 //      }
 //    }
 
-    prototypes = prototypes(program);
+    generatedPrototypes = generatePrototypes(program);
     
     // store # of prototypes so that line number reporting can be adjusted
-    prototypeCount = prototypes.size();
+    generatedPrototypeCount = generatedPrototypes.size();
   
     // do this after the program gets re-combobulated
     this.program = program;
@@ -138,7 +138,7 @@ public int writePrefix(String program, String buildPath,
     File streamFile = new File(buildPath, name + ".cpp");
     stream = new PrintStream(new FileOutputStream(streamFile));
     
-    return headerCount + prototypeCount;
+    return headerCount + generatedPrototypeCount;
   }
 
 
@@ -187,7 +187,7 @@ static String substituteUnicode(String program) {
   //public String write(String program, String buildPath, String name,
   //                  String extraImports[]) throws java.lang.Exception {
   public String write() throws java.lang.Exception {
-    writeProgram(stream, program, prototypes);
+    writeProgram(stream, program, generatedPrototypes);
     writeFooter(stream);
     stream.close();
     
@@ -195,18 +195,18 @@ public String write() throws java.lang.Exception {
   }
 
   // Write the pde program to the cpp file
-  protected void writeProgram(PrintStream out, String program, List<String> prototypes) {
-    int prototypeInsertionPoint = firstStatement(program);
+  protected void writeProgram(PrintStream out, String program, List<String> generatedPrototypes) {
+    int generatedPrototypeInsertionPoint = firstStatement(program);
   
-    out.print(program.substring(0, prototypeInsertionPoint));
+    out.print(program.substring(0, generatedPrototypeInsertionPoint));
     out.print("#include \"Arduino.h\"\n");    
     
     // print user defined prototypes
-    for (int i = 0; i < prototypes.size(); i++) {
-      out.print(prototypes.get(i) + "\n");
+    for (int i = 0; i < generatedPrototypes.size(); i++) {
+      out.print(generatedPrototypes.get(i) + "\n");
     }
     
-    out.print(program.substring(prototypeInsertionPoint));
+    out.print(program.substring(generatedPrototypeInsertionPoint));
   }
 
 
@@ -311,18 +311,35 @@ private String collapseBraces(String in) {
     return buffer.toString();
   }
   
-  public ArrayList<String> prototypes(String in) {
+  public ArrayList<String> generatePrototypes(String in) {
     in = collapseBraces(strip(in));
     
     // XXX: doesn't handle ... varargs
     // XXX: doesn't handle function pointers
-    Pattern pattern = Pattern.compile("[\\w\\[\\]\\*]+\\s+[&\\[\\]\\*\\w\\s]+\\([&,\\[\\]\\*\\w\\s]*\\)(?=\\s*\\{)");
+    Pattern prototypePattern = Pattern.compile("[\\w\\[\\]\\*]+\\s+[&\\[\\]\\*\\w\\s]+\\([&,\\[\\]\\*\\w\\s]*\\)(?=\\s*;)");
+    Pattern functionPattern = Pattern.compile("[\\w\\[\\]\\*]+\\s+[&\\[\\]\\*\\w\\s]+\\([&,\\[\\]\\*\\w\\s]*\\)(?=\\s*\\{)");
     
-    ArrayList<String> matches = new ArrayList<String>();
-    Matcher matcher = pattern.matcher(in);
-    while (matcher.find())
-      matches.add(matcher.group(0) + ";");
+    // Find already declared prototypes
+    ArrayList<String> prototypeMatches = new ArrayList<String>();
+    Matcher prototypeMatcher = prototypePattern.matcher(in);
+    while (prototypeMatcher.find())
+      prototypeMatches.add(prototypeMatcher.group(0) + ";");
+    
+    // Find all functions and generate prototypes for them
+    ArrayList<String> functionMatches = new ArrayList<String>();
+    Matcher functionMatcher = functionPattern.matcher(in);
+    while (functionMatcher.find())
+      functionMatches.add(functionMatcher.group(0) + ";");
+    
+    // Remove generated prototypes that exactly match ones found in the source file
+    for (int functionIndex=0; functionIndex < functionMatches.size(); functionIndex++) {
+      for (int prototypeIndex=0; prototypeIndex < prototypeMatches.size(); prototypeIndex++) {
+        if ((functionMatches.get(functionIndex)).equals(prototypeMatches.get(prototypeIndex))) {
+            functionMatches.remove(functionIndex);
+        }
+      }
+    }
     
-    return matches;
+    return functionMatches;
   }
 }