Which version Xilinx ISE to build hostmot2 firmware?

If you use the GUI the reason you need to add the new pinout file to the library
is that this is the only way the build system knows where to look for the source file
(you will notice that in the top level VHDL file that included packages are not
referenced by file name/path but rather the VHDL package name in the source file itself)

Thanks for the feedback on the library question. The other question still remains:

Then from the design panel click on Top ---- etc. (green icon). Then scroll down and "CLONE one of the pinout files". What happens here? You have already made a modification to a file. It is not in this list. What should you Clone now?

This last process I cant understand.