Adding Docblocks throughout the project and lowering the missing docblock limit in phpci.yml to zero.

Closes #692

PHPCI/Plugin/Shell.php

@@ -37,6 +37,18 @@ class Shell implements \PHPCI\Plugin
      */
     protected $commands = array();
 
+    /**
+     * Standard Constructor
+     *
+     * $options['directory'] Output Directory. Default: %BUILDPATH%
+     * $options['filename']  Phar Filename. Default: build.phar
+     * $options['regexp']    Regular Expression Filename Capture. Default: /\.php$/
+     * $options['stub']      Stub Content. No Default Value
+     *
+     * @param Builder $phpci
+     * @param Build   $build
+     * @param array   $options
+     */
     public function __construct(Builder $phpci, Build $build, array $options = array())
     {
         $this->phpci = $phpci;