I've followed through on the documentation found here for producing themes in 4.2 using Cmd 3.1.0. http://docs.sencha.com/ext-js/4-2/#!/guide/theming
According to the documentation. You should be able to update the development version [workspace]/[app]/index.html with these overrides using 'sencha app refresh'.
I think there may be a step missing, either that or I have done something wrong. I had to add in
To my index.html file so that my overrides work when building my application. Is this the correct way to do this? or am I doing something wrong?