diff --git a/project.properties b/project.properties
index d4e378d..d7c14df 100644
--- a/project.properties
+++ b/project.properties
@@ -1,6 +1,6 @@
-#Fri, 09 Sep 2011 14:26:03 -0500
+#Fri, 09 Sep 2011 14:55:32 -0500
 name=jlp
 version=0.3
-build.number=1
+build.number=7
 lib.local=true
 release.dir=release
diff --git a/src/main/com/jdblabs/jlp/JLPBaseGenerator.groovy b/src/main/com/jdblabs/jlp/JLPBaseGenerator.groovy
index 91f0697..320fb17 100644
--- a/src/main/com/jdblabs/jlp/JLPBaseGenerator.groovy
+++ b/src/main/com/jdblabs/jlp/JLPBaseGenerator.groovy
@@ -11,14 +11,6 @@ public abstract class JLPBaseGenerator {
     protected JLPBaseGenerator(Processor processor) {
         this.processor = processor }
 
-    protected String generate(SourceFile source) {
-
-        // run the parse phase
-        parse(source)
-
-        // run the emit phase
-        return emit(source) }
-
     protected void parse(SourceFile sourceFile) {
         sourceFile.blocks.each { block -> parse(block) } }
 
diff --git a/src/main/com/jdblabs/jlp/LiterateMarkdownGenerator.groovy b/src/main/com/jdblabs/jlp/LiterateMarkdownGenerator.groovy
index ae4d2a2..054e950 100644
--- a/src/main/com/jdblabs/jlp/LiterateMarkdownGenerator.groovy
+++ b/src/main/com/jdblabs/jlp/LiterateMarkdownGenerator.groovy
@@ -199,17 +199,17 @@ public class LiterateMarkdownGenerator extends JLPBaseGenerator {
 
             // The link should point to a different document.
             else {
-                thisDoc = processor.currentDoc
-                linkDoc = processor.docs[link.sourceDocId]
+                TargetDoc thisDoc = processor.currentDoc
+                TargetDoc linkDoc = processor.docs[link.sourceDocId]
 
-                pathToLinkedDoc = processor.getRelativePath(
+                String pathToLinkedDoc = processor.getRelativeFilepath(
                     thisDoc.sourceFile.parentFile,
-                    thatDoc.sourceFile)
+                    linkDoc.sourceFile)
 
                 // The target document may not be in the same directory
                 // as us, backtrack to the (relative) top of our directory
                 // structure.
-                newLink = pathToLinkedDoc + "/" + ".html#${linkId}" }
+                newLink = pathToLinkedDoc + ".html#${linkId}" }
                 
             return newLink }
 
diff --git a/src/main/com/jdblabs/jlp/Processor.groovy b/src/main/com/jdblabs/jlp/Processor.groovy
index 82ec9c5..958a3e6 100644
--- a/src/main/com/jdblabs/jlp/Processor.groovy
+++ b/src/main/com/jdblabs/jlp/Processor.groovy
@@ -66,13 +66,22 @@ public class Processor {
             currentDoc.sourceAST = parseRunner.run(
                 currentDoc.sourceFile.text).resultValue }
 
-        // generate output
+        // run our generator parse phase (first pass over the ASTs)
         processDocs {
 
             // TODO: add logic to configure or autodetect the correct generator
             // for each file
             def generator = getGenerator(LiterateMarkdownGenerator)
-            currentDoc.output = generator.generate(currentDoc.sourceAST) }
+            generator.parse(currentDoc.sourceAST) }
+
+
+        // Second pass by the generators, create output.
+        processDocs {
+            
+            // TODO: add logic to configure or autodetect the correct generator
+            // for each file
+            def generator = getGenerator(LiterateMarkdownGenerator)
+            currentDoc.output = generator.emit(currentDoc.sourceAST) }
 
         // Write the output to the output directory
         processDocs {