diff --git a/params/clojure/build-master.xml b/params/clojure/build-master.xml
new file mode 100644
index 0000000..54af6b9
--- /dev/null
+++ b/params/clojure/build-master.xml
@@ -0,0 +1,16 @@
+<project name="clojure-core" default="all">
+
+  <description>
+    The subsidiary autodoc build file for building the clojure core
+  </description>
+
+  <target name="all">
+    <ant dir="${src-dir}" inheritAll="false">
+      <target name="clean"/>
+      <target name="jar"/>
+    </ant>
+  </target>
+
+</project>
+
+
diff --git a/params/clojure/params.clj b/params/clojure/params.clj
index 40fe8f4..4fc9b58 100644
--- a/params/clojure/params.clj
+++ b/params/clojure/params.clj
@@ -34,7 +34,7 @@
                :version "v1.3" 
                :status "in development"
                :params {:built-clojure-jar
-                        "/home/tom/src/clj/autodoc-work-area/clojure/src/clojure-slim.jar"}}, 
+                        "/home/tom/src/clj/autodoc-work-area/clojure/src/clojure.jar"}}, 
               {:name "1.1.x" 
                :version "v1.1"
                :status "stable"
diff --git a/params/incanter/params.clj b/params/incanter/params.clj
index e1890ce..f60ce14 100644
--- a/params/incanter/params.clj
+++ b/params/incanter/params.clj
@@ -21,11 +21,13 @@
    :branches [{:name "master"
                :version "next"
                :status "in development"
-               :params {:built-clojure-jar (str root "lib/clojure-1.2.0.jar")}},
+               :params {:built-clojure-jar (str root "lib/clojure-1.2.0.jar")
+                        :load-classpath [#"/modules/[^/]+/src$"]}},
               {:name "1.0.x"
                :version "1.0"
                :status "stable"
-               :params {:built-clojure-jar (str root "lib/clojure-slim.jar")}}]
+               :params {:built-clojure-jar (str root "lib/clojure-slim.jar")
+                        :load-classpath [#"/modules/[^/]+/src/main/clojure$"]}}]
 
    :load-except-list [#"/test/" #"/classes/" #"project.clj$"],
    })
diff --git a/params/java.classpath/build.xml b/params/java.classpath/build.xml
new file mode 100644
index 0000000..ffaa3b4
--- /dev/null
+++ b/params/java.classpath/build.xml
@@ -0,0 +1,22 @@
+<project name="java.classpath" default="all">
+
+  <description>
+    The subsidiary autodoc build file for building java.classpath
+  </description>
+
+  <target name="all">
+    <!-- First clean out the lib directory so we don't get cross branch pollution -->
+    <delete>
+      <fileset dir="${src-dir}" includes="**/target/**"/>
+    </delete>
+    <mkdir dir="${src-dir}/lib"/>
+
+    <!-- now execute incanter's build/install script -->
+    <exec executable="mvn" dir="${src-dir}">
+      <arg value="test"/>
+    </exec>
+  </target>
+
+</project>
+
+
diff --git a/params/java.classpath/params.clj b/params/java.classpath/params.clj
new file mode 100644
index 0000000..534860f
--- /dev/null
+++ b/params/java.classpath/params.clj
@@ -0,0 +1,29 @@
+(import (java.io File))
+
+(let [file-prefix (.getAbsolutePath (File. "../autodoc-work-area/java.classpath"))
+      root (str file-prefix "/src/")]
+  {:name "Classpath Utilities",
+   :file-prefix file-prefix,
+   :root root,
+   :source-path "src/main/clojure",
+   :web-src-dir "https://github.com/clojure/java.classpath/blob/",
+
+   :web-home "http://clojure.github.com/java.classpath/",
+   :output-path (str file-prefix "/autodoc/"),
+   :external-doc-tmpdir "/tmp/autodoc/doc",
+;;   :clojure-contrib-classes (str root "build"),
+
+   :load-jar-dirs [(str root "lib")],
+
+   :namespaces-to-document ["clojure.java.classpath"],
+   :trim-prefix "clojure.tools.",
+
+   :branches [{:name "master"
+               :version "0.1.2"
+               :status "in development"
+               :params {:built-clojure-jar "/home/tom/src/clj/clojure-1.3/clojure.jar"}},
+              ]
+
+   :load-except-list [#"/classes/"],
+   })
+
diff --git a/params/java.classpath/templates/description.html b/params/java.classpath/templates/description.html
new file mode 100644
index 0000000..743cf01
--- /dev/null
+++ b/params/java.classpath/templates/description.html
@@ -0,0 +1,7 @@
+The classpath library provides utilities for dealing with the JVM's classpath.
+<p>
+This library is a contributed library to Clojure and can be found at
+<a href="https://github.com/clojure/java.classpath">https://github.com/clojure/java.classpath</a>.
+<p>
+Like all of Clojure and its contributed libraries, the classpath library is licensed under the 
+<a href="http://opensource.org/licenses/eclipse-1.0.php">Eclipse Public License (EPL)</a>. 
diff --git a/params/java.jdbc/build.xml b/params/java.jdbc/build.xml
new file mode 100644
index 0000000..9daac53
--- /dev/null
+++ b/params/java.jdbc/build.xml
@@ -0,0 +1,22 @@
+<project name="java.jdbc" default="all">
+
+  <description>
+    The subsidiary autodoc build file for building java.jdbc
+  </description>
+
+  <target name="all">
+    <!-- First clean out the lib directory so we don't get cross branch pollution -->
+    <delete>
+      <fileset dir="${src-dir}" includes="**/target/**"/>
+    </delete>
+    <mkdir dir="${src-dir}/lib"/>
+
+    <!-- now execute incanter's build/install script -->
+    <exec executable="mvn" dir="${src-dir}">
+      <arg value="test"/>
+    </exec>
+  </target>
+
+</project>
+
+
diff --git a/params/java.jdbc/params.clj b/params/java.jdbc/params.clj
new file mode 100644
index 0000000..c859517
--- /dev/null
+++ b/params/java.jdbc/params.clj
@@ -0,0 +1,29 @@
+(import (java.io File))
+
+(let [file-prefix (.getAbsolutePath (File. "../autodoc-work-area/java.jdbc"))
+      root (str file-prefix "/src/")]
+  {:name "JDBC-based SQL Interface",
+   :file-prefix file-prefix,
+   :root root,
+   :source-path "src/main/clojure",
+   :web-src-dir "https://github.com/clojure/java.jdbc/blob/",
+
+   :web-home "http://clojure.github.com/java.jdbc/",
+   :output-path (str file-prefix "/autodoc/"),
+   :external-doc-tmpdir "/tmp/autodoc/doc",
+
+   :load-jar-dirs [(str root "lib")],
+
+   :namespaces-to-document ["clojure.java.jdbc"],
+   :trim-prefix nil,
+   :build-json-index nil,
+
+   :branches [{:name "master"
+               :version "0.0.1"
+               :status "in development"
+               :params {:built-clojure-jar "/home/tom/src/clj/clojure-1.3/clojure.jar"}},
+              ]
+
+   :load-except-list [#"/classes/"],
+   })
+
diff --git a/params/java.jdbc/static/clojure-icon.gif b/params/java.jdbc/static/clojure-icon.gif
new file mode 100644
index 0000000..84eee16
Binary files /dev/null and b/params/java.jdbc/static/clojure-icon.gif differ
diff --git a/params/java.jdbc/static/favicon.png b/params/java.jdbc/static/favicon.png
new file mode 100644
index 0000000..b1653e8
Binary files /dev/null and b/params/java.jdbc/static/favicon.png differ
diff --git a/params/java.jdbc/templates/description.html b/params/java.jdbc/templates/description.html
new file mode 100644
index 0000000..84227df
--- /dev/null
+++ b/params/java.jdbc/templates/description.html
@@ -0,0 +1,7 @@
+java.jdbc provides a Clojure interface to SQL databases via JDBC.
+<p>
+This library is a contributed library to Clojure and can be found at
+<a href="https://github.com/clojure/java.jdbc">https://github.com/clojure/java.jdbc</a>.
+<p>
+Like all of Clojure and its contributed libraries, the JDBC library is licensed under the 
+<a href="http://opensource.org/licenses/eclipse-1.0.php">Eclipse Public License (EPL)</a>. 
diff --git a/resources/templates/master-toc.html b/resources/templates/master-toc.html
index ffd8dcc..e195044 100644
--- a/resources/templates/master-toc.html
+++ b/resources/templates/master-toc.html
@@ -6,10 +6,12 @@
       <li><a href="index.html" class="wiki_link">Overview</a></li>
       <li><a href="api-index.html" class="wiki_link">API Index</a></li>
     </ul>
-    <span class="toc-header">Namespaces</span>
-    <ul id="left-sidebar-list">
-      <li><a class="wiki_link" href="link target">Namespace short name</a></li>
-    </ul>
+    <div class="NamespaceTOC">
+      <span class="toc-header">Namespaces</span>
+      <ul id="left-sidebar-list">
+        <li><a class="wiki_link" href="link target">Namespace short name</a></li>
+      </ul>
+    </div>
     <div class="BranchTOC">
       <span class="toc-header">Other Versions</span>
       <ul id="left-sidebar-branch-list">
diff --git a/src/autodoc/build_html.clj b/src/autodoc/build_html.clj
index 903d51b..e40dcf3 100644
--- a/src/autodoc/build_html.clj
+++ b/src/autodoc/build_html.clj
@@ -214,12 +214,16 @@ looks in the base template directory."
 (deffragment make-master-toc *master-toc-file* [ns-info branch-info all-branch-info prefix]
   [:#project-name] (content (:name params))
   [:#version] (content (:version branch-info))
-  [:ul#left-sidebar-list :li] (clone-for [ns ns-info]
-                                         #(at %
+  [:div.NamespaceTOC] #(when (> (count ns-info) 1)
+                         (at %
+                             [:ul#left-sidebar-list :li]
+                             (clone-for [ns ns-info]
+                                        (fn [n]
+                                          (at n
                                               [:a] (do->
                                                     (set-attr :href (ns-html-file ns))
-                                                    (content (:short-name ns)))))
-  [:div.BranchTOC] #(when all-branch-info
+                                                    (content (:short-name ns))))))))
+  [:div.BranchTOC] #(when (> (count all-branch-info) 1)
                       (at %
                           [:ul#left-sidebar-branch-list :li]
                           (clone-for [{:keys [version name status]}
@@ -403,10 +407,11 @@ actually changed). This reduces the amount of random doc file changes that happe
         [:div#sub-namespaces]
         (substitute (map #(render-sub-namespace-api % branch-info external-docs) (:subspaces ns))))))
 
-(defn make-ns-page [ns master-toc external-docs branch-info prefix]
-  (create-page (ns-html-file ns)
+(defn make-ns-page [unique-ns? ns master-toc external-docs branch-info prefix]
+  (create-page (if unique-ns? "index.html" (ns-html-file ns))
                (when (not (:first? branch-info)) (:name branch-info))
-               (cl-format nil "~a - ~a ~a API documentation" (:short-name ns) (params :name) (:version branch-info))
+               (cl-format nil "~a - ~a ~a API documentation"
+                          (:short-name ns) (params :name) (:version branch-info))
                prefix
                master-toc
                (make-local-toc (ns-toc-data ns))
@@ -435,7 +440,7 @@ vars in ns-info that begin with that letter"
           "\n *" " ")
          suffix)))
 
-(defn gen-index-line [v ns]
+(defn gen-index-line [v ns unique-ns?]
   (let [var-name (:name v)
         overhead (count var-name)
         short-name (:short-name ns)
@@ -443,7 +448,8 @@ vars in ns-info that begin with that letter"
     #(at %
          [:a] (do->
                (set-attr :href
-                         (str (ns-html-file ns) "#" (:full-name ns) "/" (:name v)))
+                         (str (if unique-ns? "index.html" (ns-html-file ns))
+                              "#" (:full-name ns) "/" (:name v)))
                (content (:name v)))
          [:#line-content] (content 
                            (cl-format nil "~vt~a~vt~a~vt~a~%"
@@ -453,7 +459,7 @@ vars in ns-info that begin with that letter"
                                       (doc-prefix v doc-len))))))
 
 ;; TODO: skip entries for letters with no members
-(deffragment make-index-content *index-html-file* [branch-info vars-by-letter]
+(deffragment make-index-content *index-html-file* [branch-info vars-by-letter unique-ns?]
   [:#header-project] (content (:name params))
   [:#header-version] (content (:version branch-info))
   [:#header-status] (content (:status branch-info))
@@ -463,16 +469,18 @@ vars in ns-info that begin with that letter"
                          [:h2] (set-attr :id letter)
                          [:span#section-head] (content letter)
                          [:span#section-content] (clone-for [[v ns] vars]
-                                                   (gen-index-line v ns)))))
+                                                   (gen-index-line v ns unique-ns?)))))
 
 (defn make-index-html [ns-info master-toc branch-info prefix]
   (create-page *index-html-file*
                (when (not (:first? branch-info)) (:name branch-info))
-               (cl-format nil "Index - ~a ~a API documentation" (params :name) (:version branch-info))
+               (cl-format nil "Index - ~a ~a API documentation"
+                          (params :name) (:version branch-info))
                prefix
                master-toc
                nil
-               (make-index-content branch-info (vars-by-letter ns-info))))
+               (make-index-content branch-info (vars-by-letter ns-info)
+                                   (<= (count ns-info) 1))))
 
 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
 ;;;
@@ -591,9 +599,11 @@ vars in ns-info that begin with that letter"
        (let [prefix (if (:first? branch-info) nil "../")
              master-toc (make-master-toc ns-info branch-info all-branch-info prefix)
              external-docs (wrap-external-doc doc-dir master-toc)]
-         (make-overview ns-info master-toc branch-info prefix)
-         (doseq [ns ns-info]
-           (make-ns-page ns master-toc external-docs branch-info prefix))
+         (if (> (count ns-info) 1)
+           (do (make-overview ns-info master-toc branch-info prefix)
+               (doseq [ns ns-info]
+                 (make-ns-page false ns master-toc external-docs branch-info prefix)))
+           (make-ns-page true (first ns-info) master-toc external-docs branch-info prefix))
          (make-index-html ns-info master-toc branch-info prefix)
          (make-index-clj ns-info branch-info)
          (make-index-json ns-info branch-info)))))
diff --git a/src/autodoc/doc_files.clj b/src/autodoc/doc_files.clj
index e63017e..6284898 100644
--- a/src/autodoc/doc_files.clj
+++ b/src/autodoc/doc_files.clj
@@ -43,6 +43,12 @@ transformations along the way."
    (File. (File. dst) (.replaceFirst relative "\\.markdown$" ".html"))
    (:out (sh "markdown" (.getPath src-file)))))
 
+(defmethod xform-file "md"
+  [src-file dst relative]
+  (spit
+   (File. (File. dst) (.replaceFirst relative "\\.md$" ".html"))
+   (:out (sh "markdown" (.getPath src-file)))))
+
 (defn xform-tree 
   "Takes source and destination directories and copies the source to the destination,
 transforming files as appropriate."