Within a Project I am working on I want to alter the theme with the use of JQuery. What I want to do is include jQuery within the ui. However I am not fully aware of the risks. My understanding is that as long as you don't override the Global variables 'mx', 'mendix' and 'dojo' you should be fine. Any advice or outlines would be useful. Thanks!
Unless the version you load causes a jQuery version conflict in a widget that depends on a different jQuery version. That could cause some trouble.
I have used JQuery in several projects in the form widgets and in the html header. The only issue I have had is that JQuery 1.8 was incredibly slow performing in Internet Explorer 8. We upgraded to 1.10 and it solved all the slow performances. So just don't use 1.8 and you should be ok.