Updated manual to show current output of --help (#239)

Manual.html

@@ -97,7 +97,7 @@ To get usage instructions for the command line interface, type
 This displays the following information:
 This displays the following information:
 <tt><pre>
 <tt><pre>
 Usage: pdbfixer
 Usage: pdbfixer
-       pdbfixer [options] filename
+       pdbfixer filename [options]
 
 
 When run with no arguments, it launches the user interface.  If any arguments are specified, it runs in command line mode.
 When run with no arguments, it launches the user interface.  If any arguments are specified, it runs in command line mode.
 
 
@@ -125,6 +125,7 @@ Options:
   --ionic-strength=STRENGTH
   --ionic-strength=STRENGTH
                         molar concentration of ions to add to the water box
                         molar concentration of ions to add to the water box
                         [default: 0.0]
                         [default: 0.0]
+  --verbose             Print verbose output
 </pre></tt>
 </pre></tt>
 For example, consider the following command line:
 For example, consider the following command line:
 <p>
 <p>