Late response but I found this thread while searching to resolve the same issue, tried the regex solution, which didn't work for me, so came up with this solution, which is at least less drastic than disabling HTML Tidy Validator:
Window > Preferences > Aptana Studio > Validation > HTML Tidy Validator
- Change Attributes > Proprietary Attributes from Warning to either Ignore or Info.
There are several other frameworks other than jQuery Mobile (Angular for example) where the use of custom attributes is common, so I don't think this is a bad thing to do, as I don't know of any browser that breaks with custom attributes, they just get ignored.
While you're changing HTML Tidy Validator, I'd also recommend removing the warning for elements with no content as often folks populate those through JavaScript. You can do so like this:
- Change Elements > Trim Empty Elements from Warning to either Ignore or Info.