Updated parseVarargin to avoid that weird first logical argument.

Now can call the function with a 'help' argument, like so:
myFun('help').
parseVarargin now ignores the 'ans' variable when displaying help
Indentation.
Disabling everything when Java isn't available.

Ideally, if Java isn't available, this should be replaced by a command-line type thing. This sounds too painful to implement for now.
Fixed issue when Java is disabled.
Added TODO in comments.
Fixed typo when 'images' is chosen.
Turning off multicore debug by default.
Added support for NaNs when loading from XML.