Hi!
My build leaves files such as
./common/.fdt_support.o.cmd ./common/.console.o.cmd ./common/.main.o.cmd ./common/.cmd_load.o.cmd ./common/.flash.o.cmd ./common/.env_flags.o.cmd ./common/.cmd_source.o.cmd ./common/.built-in.o.cmd
. Git usage would be slightly nicer if those were ignored. My u-boot is based on v2013.01.01... hmm. I expected Altera to have slightly newer version. That may explain stuff.
.*.cmd files were introduced by Kbuild at v2014.04-rc1 and correctly ignored. v2013.01.01 you are using has nothing to do with Kbuild.
I guess you built at u-boot/master (.*.cmd files were generated) and then you checked out v2013.01.01.
Yes, I guess that's what happened.
And one more thing. Your patch is not applicable at all. Please do not post a patch based on such an old tag.
Sorry for the noise, Pavel