Issue 51

[LilyAndres]

Address #51 changed the templates using LibreOffice, I didn't use google docs because I had some issues before.
I also changed the design pattern yaml file by removing 'plant structure' for 'material entity'.
I also ran the steps in the wiki "Intermediate CDNO Compile Instructions", so two owl files have been updated as well.
I created templates/include/BFO_includes.txt file

Could you please have a look @kaiiam? I hope these changes are ok, we can discuss about it, thanks.

[kaiiam]

Working with @LilyAndres we've updated the command in https://github.com/Southern-Cross-Plant-Science/cdno/wiki/Intermediate-CDNO-Compile-Instructions to replace PO plant structure with BFO material entity. This is now working in this PR having updated everything. However we now have the issue that some classes are asserted as subclass to material entity when we only want them to show up in cdno-edit.owl as subclass to the appropriate terms from the dietary nutritional component hierarchy.

We've decided to merge this for now, but we'll need to make a new issue/PR to deal with this.