Being a newbie to webkit, I was thrown for a loop thinking that after I did a command line build I could then "build" in webkit. When you do this it breaks your command line build and you are no longer able to do anything.
bdash (via IRC) aksed I submit this bug report
I suggest a note be added ot the linked page which is something like this"
NOTE: Debugging is possible via xcode, but building from xcode will not work correctly without additional configuration. If you accidentially attempt to build in xcode, you will need to re run the build-webkit script from the command line"
Notes were added at some point in the past. The new website includes these notes.