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:
 <tt><pre>
 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.
 
@@ -125,6 +125,7 @@ Options:
   --ionic-strength=STRENGTH
                         molar concentration of ions to add to the water box
                         [default: 0.0]
+  --verbose             Print verbose output
 </pre></tt>
 For example, consider the following command line:
 <p>