How to get bare metal app running independently on SoCkit?

There is actually a good example in the "Hello World" example at this link: http://www.alterawiki.com/wiki/socbootfromfpga

It really all depends what you mean by "bare metal". You can probably get your code running in the On-Chip Memory by replacing the preloader with your own code and placing your code in the 0xA2 partition, but you'll have to do any chip initialization yourself. I haven't seen any good examples yet on working with no preloader, even though there is no particular reason why you couldn't.

You could even build an RTOS in DS-5 and port it over, if you wanted to try that.