Template files: fix various links

Verified all remaining links and updated them where necessary.

Note: I've stayed away from updating links in the docblocks of external dependencies, like JS libraries. Those should be automatically updated when those libraries are updated (which they probably should be).

data/templates/clean/css/phpdocumentor-clean-icons/Read Me.txt

@@ -1,3 +1,3 @@
 To modify your generated font, use the *dev.svg* file, located in the *fonts* folder in this package. You can import this dev.svg file to the IcoMoon app. All the tags (class names) and the Unicode points of your glyphs are saved in this file.
 
-See the documentation for more info on how to use this package: http://icomoon.io/#docs/font-face
+See the documentation for more info on how to use this package: https://icomoon.io/#docs/font-face

data/templates/clean/htaccess.dist

@@ -1,4 +1,4 @@
-# Fixes a vulnerability in CentOS: http://stackoverflow.com/questions/20533279/prevent-php-from-parsing-non-php-files-such-as-somefile-php-txt
+# Fixes a vulnerability in CentOS: https://stackoverflow.com/questions/20533279/
 <FilesMatch \.php\.txt$>
     RemoveHandler .php
     ForceType text/plain

data/templates/guides/rtd/html/layout.html.twig

@@ -34,7 +34,7 @@
     <link rel="stylesheet" href="{{ asset('css/theme.css') }}" type="text/css"/>
     <link rel="stylesheet" href="{{ asset('css/badge_only.css') }}" type="text/css"/>
 
-    {# Keep modernizr in head - http://modernizr.com/docs/#installing #}
+    {# Keep modernizr in head - https://modernizr.com/docs/#installing #}
     <script src="{{ asset('js/modernizr.min.js') }}"></script>
 
 </head>

data/templates/responsive-twig/js/template.js

@@ -145,7 +145,7 @@ $(document).ready(function() {
         $("body > .container").prepend(
             '<div class="alert alert-error"><a class="close" data-dismiss="alert">×</a>' +
             'You are using Google Chrome in a local environment; AJAX interaction has been ' +
-            'disabled because Chrome cannot <a href="http://code.google.com/p/chromium/issues/detail?id=40787">' +
+            'disabled because Chrome cannot <a href="https://bugs.chromium.org/p/chromium/issues/detail?id=40787">' +
             'retrieve files using Ajax</a>.</div>'
         );
     }

data/templates/responsive-twig/layout.html.twig

@@ -117,8 +117,8 @@
 
     {% block footer %}
     <footer class="span12">
-            Template is built using <a href="http://twitter.github.com/bootstrap/">Twitter Bootstrap 2</a> and icons provided by
-            <a href="http://glyphicons.com/">Glyphicons</a>.<br/>
+            Template is built using <a href="https://getbootstrap.com/">Twitter Bootstrap 2</a> and icons provided by
+            <a href="https://glyphicons.com/">Glyphicons</a>.<br/>
             Documentation is powered by <a href="https://www.phpdoc.org/">phpDocumentor {{ version }}</a> and<br/>
             generated on {{ now|date("r") }}.<br/>
     </footer>