fix up repo links

README.md

@@ -11,9 +11,9 @@ Marginalia 0.9.1
 
 Marginalia is a source code documentation tool that parses Clojure and ClojureScript code and outputs a side-by-side source view with appropriate comments and docstrings aligned.
 
-To get a quick look at what the Marginalia output looks like, [visit the official site](http://gdeer81.github.io/marginalia/).
+To get a quick look at what the Marginalia output looks like, **visit the official site** _[we're working on getting a version of this back up and running!]_.
 
-**[View the release notes for this version of Marginalia](https://github.com/gdeer81/marginalia/blob/master/docs/release-notes/marginalia-v0.9.1-release-notes.markdown)**
+**[View the release notes for this version of Marginalia](https://github.com/clj-commons/marginalia/blob/master/docs/release-notes/marginalia-v0.9.1-release-notes.markdown)**
 
 Usage
 -----
@@ -22,13 +22,13 @@ Currently Marginalia can be used in a number of ways as described below.
 
 ### Leiningen
 
-[http://github.com/gdeer81/lein-marginalia](http://github.com/gdeer81/lein-marginalia)
+[https://github.com/clj-commons/lein-marginalia](https://github.com/clj-commons/lein-marginalia)
 
 To use Marginalia with Leiningen add the following code to the project's `project.clj` file:
 
 With Leiningen 1.x, add `[lein-marginalia "0.9.1"]` to your project.clj's `:dev-dependencies` argument of the `defproject` function, then run `lein deps`.
 With Leiningen 2.x, add `[[lein-marginalia "0.9.1"]]` to the `:plugins` entry in either your project.clj file or your `:user` profile.
-See the [lein-marginalia](http://github.com/gdeer81/lein-marginalia) page for more details.
+See the [lein-marginalia](https://github.com/clj-commons/lein-marginalia) page for more details.
 
 Once installed,  you can generate your complete source documentation with the command:
 

docs/release-notes/marginalia-v0.7.0-release-notes.markdown

@@ -5,21 +5,21 @@ Marginalia is an ultra-lightweight literate programming tool for Clojure inspire
 
 To get a quick look at what the output looks like, [visit the official Marginalia website](http://fogus.me/fun/marginalia/).
 
-**Usage notes and examples are found on the [Marginalia Github page](http://github.com/fogus/marginalia).**
+**Usage notes and examples are found on the [Marginalia Github page](https://github.com/clj-commons/marginalia).**
 
 Places
 ------
 
-* [Source code](https://github.com/fogus/marginalia)
-* [Ticket system](https://github.com/fogus/marginalia/issues)
+* [Source code](https://github.com/clj-commons/marginalia)
+* [Ticket system](https://github.com/clj-commons/marginalia/issues)
 * [manifesto](http://blog.fogus.me/2011/01/05/the-marginalia-manifesto/)
 
 Changes from v6.0.1
 -------------------
 
 ### lein-marginalia
 
-Version 0.7.0 is an attempt to move toward Marginalia as library only.  Therefore, the Leiningen support has been pulled out and placed into its own plugin named [lein-marginalia](http://github.com/fogus/lein-marginalia).  To use Marginalia to generate documentation for your own projects you should no longer reference Marginalia in your `project.clj`.  Instead, use lein-marginalia in your `:dev-dependencies` section like so:
+Version 0.7.0 is an attempt to move toward Marginalia as library only.  Therefore, the Leiningen support has been pulled out and placed into its own plugin named [lein-marginalia](https://github.com/fogus/lein-marginalia).  To use Marginalia to generate documentation for your own projects you should no longer reference Marginalia in your `project.clj`.  Instead, use lein-marginalia in your `:dev-dependencies` section like so:
 
     :dev-dependencies [[lein-marginalia "0.7.0"]]
 
@@ -48,10 +48,10 @@ You can pass any number of arguments to the `marg` task.
 ### Bug fixes
 
 * Prefixed keywords (#54 and #87)
-* [`project.clj` requirement](https://github.com/fogus/marginalia/issues/20)
-* [`^:private support`](https://github.com/fogus/marginalia/issues/49)
-* [Comment code blocks](https://github.com/fogus/marginalia/issues/50)
-* [`:requires` bug](https://github.com/fogus/marginalia/issues/55)
+* [`project.clj` requirement](https://github.com/clj-commons/marginalia/issues/20)
+* [`^:private support`](https://github.com/clj-commons/marginalia/issues/49)
+* [Comment code blocks](https://github.com/clj-commons/marginalia/issues/50)
+* [`:requires` bug](https://github.com/clj-commons/marginalia/issues/55)
 
 
 Plans
@@ -61,7 +61,7 @@ The following capabilities are under design, development, or consideration for f
 
 * protocol docstring support
 * Stand-alone application
-* Explore the possibility of leveraging the [ClojureScript](http://github.com/clojure/clojurescript) analyzer.
+* Explore the possibility of leveraging the [ClojureScript](https://github.com/clojure/clojurescript) analyzer.
 * More documentation and examples
 
 More planning is needed around capabilities not listed nor thought of.

docs/release-notes/marginalia-v0.7.1-release-notes.markdown

@@ -5,21 +5,21 @@ Marginalia is an ultra-lightweight literate programming tool for Clojure and Clo
 
 To get a quick look at what the output looks like, [visit the official Marginalia website](http://fogus.me/fun/marginalia/).
 
-**Usage notes and examples are found on the [Marginalia Github page](http://github.com/fogus/marginalia).**
+**Usage notes and examples are found on the [Marginalia Github page](https://github.com/clj-commons/marginalia).**
 
 Places
 ------
 
-* [Source code](https://github.com/fogus/marginalia)
-* [Ticket system](https://github.com/fogus/marginalia/issues)
+* [Source code](https://github.com/clj-commons/marginalia)
+* [Ticket system](https://github.com/clj-commons/marginalia/issues)
 * [manifesto](http://blog.fogus.me/2011/01/05/the-marginalia-manifesto/)
 
 Changes from v7.0.0
 -------------------
 
 ### lein-marginalia
 
-As always, the prefered way to use Marginalia to generate your documentation is via the [lein-marginalia](http://github.com/fogus/lein-marginalia) Leiningen plugin, like so:
+As always, the prefered way to use Marginalia to generate your documentation is via the [lein-marginalia](https://github.com/fogus/lein-marginalia) Leiningen plugin, like so:
 
     :dev-dependencies [[lein-marginalia "0.7.1"]]
 
@@ -43,7 +43,7 @@ The following capabilities are under design, development, or consideration for f
 * Nicer looking `toc.html` generation in `--multi` mode output.
 * protocol docstring support
 * Stand-alone application
-* Explore the possibility of leveraging the [ClojureScript](http://github.com/clojure/clojurescript) analyzer.
+* Explore the possibility of leveraging the [ClojureScript](https://github.com/clojure/clojurescript) analyzer.
 * Explore the possibility of leveraging [sjacket](https://github.com/cgrand/sjacket)
 * More documentation and examples
 

docs/release-notes/marginalia-v0.8.0-release-notes.markdown

@@ -5,21 +5,21 @@ Marginalia is an ultra-lightweight literate programming tool for Clojure and Clo
 
 To get a quick look at what the output looks like, [visit the official Marginalia website](http://fogus.me/fun/marginalia/).
 
-**Usage notes and examples are found on the [Marginalia Github page](http://github.com/gdeer81/marginalia).**
+**Usage notes and examples are found on the [Marginalia Github page](https://github.com/clj-commons/marginalia).**
 
 Places
 ------
 
-* [Source code](https://github.com/gdeer81/marginalia)
-* [Ticket system](https://github.com/gdeer81/marginalia/issues)
+* [Source code](https://github.com/clj-commons/marginalia)
+* [Ticket system](https://github.com/clj-commons/marginalia/issues)
 * [manifesto](http://blog.fogus.me/2011/01/05/the-marginalia-manifesto/)
 
 Changes from v0.7.1
 -------------------
 
 ### lein-marginalia
 
-As always, the prefered way to use Marginalia to generate your documentation is via the [lein-marginalia](http://github.com/fogus/lein-marginalia) Leiningen plugin, like so:
+As always, the prefered way to use Marginalia to generate your documentation is via the [lein-marginalia](https://github.com/fogus/lein-marginalia) Leiningen plugin, like so:
 
     :dev-dependencies [[lein-marginalia "0.8.0"]]
 
@@ -33,7 +33,7 @@ Marginalia has long supported the generation of documentation where each namespa
 
 * :url in project-info now creates a hyperlink for the project name
 * Support for ClojureScript's data literals!
-* Suppress comment parsing through [directives](https://github.com/gdeer81/marginalia/pull/126)
+* Suppress comment parsing through [directives](https://github.com/clj-commons/marginalia/pull/126)
 * Floating-toc HTML in generated uberdoc
 * Sort files by namespace
 * Improved handling of ClojureScript files
@@ -47,7 +47,7 @@ The following capabilities are under design, development, or consideration for f
 
 * Nicer looking `toc.html` generation in `--multi` mode output.
 * protocol docstring support
-* Explore the possibility of leveraging the [ClojureScript](http://github.com/clojure/clojurescript) analyzer.
+* Explore the possibility of leveraging the [ClojureScript](https://github.com/clojure/clojurescript) analyzer.
 * Explore the possibility of leveraging [sjacket](https://github.com/cgrand/sjacket)
 * More documentation and examples
 

docs/release-notes/marginalia-v0.9.1-release-notes.markdown

@@ -5,21 +5,21 @@ Marginalia is an ultra-lightweight literate programming tool for Clojure and Clo
 
 To get a quick look at what the output looks like, [visit the official Marginalia website](http://fogus.me/fun/marginalia/).
 
-**Usage notes and examples are found on the [Marginalia Github page](http://github.com/gdeer81/marginalia).**
+**Usage notes and examples are found on the [Marginalia Github page](https://github.com/clj-commons/marginalia).**
 
 Places
 ------
 
-* [Source code](https://github.com/gdeer81/marginalia)
-* [Ticket system](https://github.com/gdeer81/marginalia/issues)
+* [Source code](https://github.com/clj-commons/marginalia)
+* [Ticket system](https://github.com/clj-commons/marginalia/issues)
 * [manifesto](http://blog.fogus.me/2011/01/05/the-marginalia-manifesto/)
 
 Changes from v0.8.0
 -------------------
 
 ### lein-marginalia
 
-As always, the prefered way to use Marginalia to generate your documentation is via the [lein-marginalia](http://github.com/fogus/lein-marginalia) Leiningen plugin, like so:
+As always, the prefered way to use Marginalia to generate your documentation is via the [lein-marginalia](https://github.com/fogus/lein-marginalia) Leiningen plugin, like so:
 
     :dev-dependencies [[lein-marginalia "0.9.1"]]
 
@@ -34,7 +34,7 @@ Marginalia has long supported the generation of documentation where each namespa
 * Fix no newline at the end of parser.clj.
 * Fix no namespace extracted from .cljx files.
 * Add support for cljx reader tags #+clj and #+cljs to make it possible
-* handle (ignore) extra args from LispReader 
+* handle (ignore) extra args from LispReader
 * fixed regex helper
 
 
@@ -45,7 +45,7 @@ The following capabilities are under design, development, or consideration for f
 
 * Nicer looking `toc.html` generation in `--multi` mode output.
 * protocol docstring support
-* Explore the possibility of leveraging the [ClojureScript](http://github.com/clojure/clojurescript) analyzer.
+* Explore the possibility of leveraging the [ClojureScript](https://github.com/clojure/clojurescript) analyzer.
 * Explore the possibility of leveraging [sjacket](https://github.com/cgrand/sjacket)
 * More documentation and examples
 

docs/uberdoc.html

@@ -3271,7 +3271,7 @@ <h2>The one true way</h2>
 like this:</p>
 
 <pre><code>:marginalia {
-  :javascript 
+  :javascript
     ["http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"]}
 </code></pre>
 
@@ -3506,7 +3506,7 @@ <h2>The one true way</h2>
       content]
      [:div {:class &quot;footer&quot;}
       &quot;Generated by &quot;
-      [:a {:href &quot;https://github.com/gdeer81/marginalia&quot;} &quot;Marginalia&quot;]
+      [:a {:href &quot;https://github.com/clj-commons/marginalia&quot;} &quot;Marginalia&quot;]
       &quot;.&amp;nbsp;&amp;nbsp;&quot;
       &quot;Syntax highlighting provided by Alex Gorbatchev's &quot;
       [:a {:href &quot;http://alexgorbatchev.com/SyntaxHighlighter/&quot;}
@@ -3552,7 +3552,7 @@ <h2>The one true way</h2>
 </td><td class="codes"><pre class="brush: clojure">(defn public-fn  []
   (let [x (private-fn)]
         (count x)))</pre></td></tr><tr><td class="docs"><p>Should have only this comment in the left margin.
-See <a href="https://github.com/gdeer81/marginalia/issues/4">https://github.com/gdeer81/marginalia/issues/4</a></p>
+See <a href="https://github.com/clj-commons/marginalia/issues/4">https://github.com/clj-commons/marginalia/issues/4</a></p>
 </td><td class="codes"></td></tr><tr><td class="docs">
 </td><td class="codes"><pre class="brush: clojure">(defn parse-bool [v] (condp = (.trim (str v))
                          &quot;0&quot; false
@@ -3669,7 +3669,7 @@ <h2>The one true way</h2>
 </td><td class="codes"><pre class="brush: clojure">(defmulti ns-kw-mm identity)
 (defmethod ns-kw-mm ::foo [_] :problem-cases.general/foo)
 (defmethod ns-kw-mm :user/foo [_] :user/foo)
-(defmethod ns-kw-mm :foo [_] :foo)</pre></td></tr><tr><td class="spacer docs">&nbsp;</td><td class="codes" /></tr></table><div class="footer">Generated by <a href="https://github.com/gdeer81/marginalia">Marginalia</a>.&nbsp;&nbsp;Syntax highlighting provided by Alex Gorbatchev's <a href="http://alexgorbatchev.com/SyntaxHighlighter/">SyntaxHighlighter</a><div id="floating-toc"><ul><li class="floating-toc-li" id="floating-toc_marginalia.core">marginalia.core</li><li class="floating-toc-li" id="floating-toc_marginalia.html">marginalia.html</li><li class="floating-toc-li" id="floating-toc_problem-cases.general">problem-cases.general</li></ul></div></div><script type="text/javascript">SyntaxHighlighter.defaults['gutter'] = false;
+(defmethod ns-kw-mm :foo [_] :foo)</pre></td></tr><tr><td class="spacer docs">&nbsp;</td><td class="codes" /></tr></table><div class="footer">Generated by <a href="https://github.com/clj-commons/marginalia">Marginalia</a>.&nbsp;&nbsp;Syntax highlighting provided by Alex Gorbatchev's <a href="http://alexgorbatchev.com/SyntaxHighlighter/">SyntaxHighlighter</a><div id="floating-toc"><ul><li class="floating-toc-li" id="floating-toc_marginalia.core">marginalia.core</li><li class="floating-toc-li" id="floating-toc_marginalia.html">marginalia.html</li><li class="floating-toc-li" id="floating-toc_problem-cases.general">problem-cases.general</li></ul></div></div><script type="text/javascript">SyntaxHighlighter.defaults['gutter'] = false;
 SyntaxHighlighter.all();
 
 // hackity hack

src/marginalia/html.clj

@@ -135,7 +135,7 @@
 ;; like this:
 ;;
 ;;     :marginalia {
-;;       :javascript 
+;;       :javascript
 ;;         ["http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"]}
 ;;
 ;; That way you won't have to download and carry around the MathJax library.
@@ -385,7 +385,7 @@
       content]
      [:div {:class "footer"}
       "Generated by "
-      [:a {:href "https://github.com/gdeer81/marginalia"} "Marginalia"]
+      [:a {:href "https://github.com/clj-commons/marginalia"} "Marginalia"]
       ".  "
       "Syntax highlighting provided by Alex Gorbatchev's "
       [:a {:href "http://alexgorbatchev.com/SyntaxHighlighter/"}

src/problem_cases/general.clj

@@ -13,7 +13,7 @@
         (count x)))
 
 ;; Should have only this comment in the left margin.
-;; See [https://github.com/gdeer81/marginalia/issues/4](https://github.com/gdeer81/marginalia/issues/4)
+;; See [https://github.com/clj-commons/marginalia/issues/4](https://github.com/clj-commons/marginalia/issues/4)
 
 (defn parse-bool [v] (condp = (.trim (str v))
                          "0" false