Just cloned this and ran index.html on a local http server (mongoose) in Chrome 25. When I click one of the links in the footer I get various errors in the console:
http://localhost/jqmobile/boiler/ AppBoilerplate.js:93
loaded first plugin sample_plugin.js:8
http://localhost/jqmobile/boiler/ AppBoilerplate.js:93
GET http://localhost/jqmobile/boiler/app/extensions/http://localhost/jqmobile/boiler/app/extensions/sample_plugin/sample_plugin.js 404 (Not Found) require.js:1834
Uncaught Error: Script error
http://requirejs.org/docs/errors.html#scripterror require.js:160
GET http://localhost/jqmobile/boiler/app/extensions/http://localhost/jqmobile/boiler/app/extensions/theme_switcher/theme_switcher.js 404 (Not Found) require.js:1834
Uncaught Error: Script error
http://requirejs.org/docs/errors.html#scripterror require.js:160
It seems to be building the paths incorrectly.
PS: the jqMobile css loads a little late so you initially see an unstyled page. I've not seen this happen before with jqMobile in the past (v1.1).