The step-by-step guide is helpful, but I think only in the case where you just want to create a copy of the KSDK example in the same folder as the rest of the examples. For those that have a different working directory (e.g. something under version control), then I think you have three options:
1. use symbolic links to fake out either KDS or your VCS so that the files can go under version control in your workspace directory, while KDS still thinks all of the relative paths are correct
2. wait for an updated tool like the one Iva has created
3. use a manual process, which takes a bit of time, but will still work. In a nutshell, it involves using the Import feature to import an existing example into your working directory. You'll then need to edit the .project and .cproject files to fix the virtual file pointers and the relative paths to the include folders. I use the ${KSDK_PATH} variable and then do a search and replace on everything that is relative to ${ProjDirPath} so that the include folders can be located by the compiler. The same goes for the linker settings. Generally speaking, once you've done this you can get an example working. It took me a bit of time to figure all of this out, but I have a couple of projects based loosely on demo projects and have them running in a completely separate working directory.