diff --git a/jlp b/jlp
new file mode 100755
index 0000000..5b0198c
--- /dev/null
+++ b/jlp
@@ -0,0 +1 @@
+ng com.jdblabs.jlp.JLPMain "$@"
diff --git a/lib/runtime/jar/commons-cli-1.2.jar b/lib/runtime/jar/commons-cli-1.2.jar
new file mode 100644
index 0000000..ce4b9ff
Binary files /dev/null and b/lib/runtime/jar/commons-cli-1.2.jar differ
diff --git a/lib/runtime/jar/groovy-all-1.7.10.jar b/lib/runtime/jar/groovy-all-1.7.10.jar
new file mode 100644
index 0000000..b4f77c9
Binary files /dev/null and b/lib/runtime/jar/groovy-all-1.7.10.jar differ
diff --git a/project.properties b/project.properties
index 7500dab..3592935 100644
--- a/project.properties
+++ b/project.properties
@@ -1,4 +1,5 @@
+#Tue, 06 Sep 2011 17:09:38 -0500
 name=jlp
 version=alpha1
-build.number=0
+build.number=6
 lib.local=true
diff --git a/resources/main/jlp.css b/resources/main/jlp.css
index bcff1ad..ed78184 100644
--- a/resources/main/jlp.css
+++ b/resources/main/jlp.css
@@ -50,7 +50,7 @@ td.docs, th.docs {
 
 .docs table {
     border: thin solid #dedede;
-    margin-left: 30px; }
+    margin-left: 60px; }
 
 td.code, th.code {
     padding: 14px 15px 16px 25px;
diff --git a/src/main/com/jdblabs/jlp/JLPMain.groovy b/src/main/com/jdblabs/jlp/JLPMain.groovy
index 147cbaa..8f69855 100644
--- a/src/main/com/jdblabs/jlp/JLPMain.groovy
+++ b/src/main/com/jdblabs/jlp/JLPMain.groovy
@@ -1,6 +1,7 @@
 package com.jdblabs.jlp
 
 import com.jdblabs.jlp.ast.ASTNode
+import com.jdblabs.jlp.ast.SourceFile
 import org.parboiled.Parboiled
 import org.parboiled.parserunners.ReportingParseRunner
 
@@ -18,6 +19,8 @@ public class JLPMain {
 
         // define options
         cli.h('Print this help information.', longOpt: 'help', required: false)
+        cli.o("Output directory (defaults to 'jlp-docs').",
+            longOpt: 'output-dir', required: false)
 
         // parse options
         def opts = cli.parse(args)
@@ -27,31 +30,62 @@ public class JLPMain {
             cli.usage()
             return }
 
+        // get the output directory and create it if necessary
+        def outputDir = opts.o ? new File(opts.o) : new File("jlp-docs")
+        if (!outputDir.exists()) outputDir.mkdirs()
+
+        // get the CSS theme to use
+        def css = JLPMain.class.getResourceAsStream("/jlp.css") // TODO: make an option
+        css = css.text
+
         // get files passed in
         def filenames = opts.getArgs()
-        def files = filenames.collect { new File(it) }
         
         // -------- parse input -------- //
-        Map parsedFiles = files.inject([:]) { acc, file ->
-            def parsed = inst.parse(new File(file))
-            acc[file.canonicalPath] = parsed
+        Map parsedFiles = filenames.inject([:]) { acc, filename ->
+            acc[filename] = inst.parse(new File(filename))
             return acc }
 
         // -------- generate output -------- //
+        Map htmlDocs = LiterateMarkdownGenerator.generateDocuments(parsedFiles)
+
+        // -------- write output files ------- //
+        htmlDocs.each { filename, html ->
+            // split the path into parts
+            def fileParts = filename.split(/[\.\/]/)
+
+            File subDir = new File('.')
+
+            if (fileParts.length > 2) {
+                // find the relative subdirectory of this file
+                subDir = new File(outputDir, fileParts[0..-3].join('/'))
+                if (!subDir.exists()) subDir.mkdirs()
+            }
+
+            // recreate the output filename
+            def outputFilename = fileParts[-2] + ".html"
+
+            // write the HTML to the file
+            new File(subDir, outputFilename).withWriter { fileOut ->
+
+                // write the CSS if it is not present
+                File cssFile = new File(subDir, "jlp.css")
+                if (!cssFile.exists()) cssFile.withWriter { cssOut ->
+                    cssOut.println css }
+
+
+                // write the file
+                fileOut.println html } }
     }
 
     public JLPMain() {
         parser = Parboiled.createParser(JLPPegParser.class)
     }
 
-    public Map parse(File inputFile) {
+    public SourceFile parse(File inputFile) {
         def parseRunner = new ReportingParseRunner(parser.SourceFile())
 
         // parse the file
-        return parseRunner.run(inputFile).resultValue
-    }
-
-    public def generate(def emitter, List<ASTNode> blocks) {
-        // second pass, semantics
+        return parseRunner.run(inputFile.text).resultValue
     }
 }
diff --git a/src/main/com/jdblabs/jlp/LiterateMarkdownGenerator.groovy b/src/main/com/jdblabs/jlp/LiterateMarkdownGenerator.groovy
index 0422f86..db45fd8 100644
--- a/src/main/com/jdblabs/jlp/LiterateMarkdownGenerator.groovy
+++ b/src/main/com/jdblabs/jlp/LiterateMarkdownGenerator.groovy
@@ -50,7 +50,7 @@ public class LiterateMarkdownGenerator extends JLPBaseGenerator {
     <head>
         <title>${docState.currentDocId}</title>
         <meta http-equiv="content-type" content="text/html; charset=UTF-8">
-        <link rel="stylesheet" media="all" href="docco.css"/>
+        <link rel="stylesheet" media="all" href="jlp.css"/>
     </head>
     <body>
         <div id="container">