Hi Arnon,
Still working on the trees. Will take me a few more days to get to the bottom of an issue that was recently identified. 
Have you seen this tutorial? There are small files you can use as a demo, and it also mentions the "full size files"
I agree, the tutorial could use more description of what the files are, and not just the commands used. Thanks for bringing this up. I need to expand some of the documentation.
The paper might also help clarify things:
The foundation tree is a tree built from an alignment database for an evolutionarily conserved marker gene (like the 18S for the fungal example) that can be aligned across distant taxonomic lineages to build a “foundation” tree. It's the tree that you will use to graft your extension sequences onto. When you have sequences such as ITS that are good at taxonomic identification but that make terrible alignments across all lineages (but ITS does make good alignments for closely related organisms, and it has good taxonomic resolution/identification), you don't just want to make a tree from all of your ITS seqs....so ghost-tree grafts them onto the foundation to build a hybrid-gene tree that has the benefits of both ITS and 18S gene regions. Please note that the foundation can be either a tree or an alignment but you have to choose the right subcommand in ghost-tree.
Silva 18S is a good foundation tree for fungal ITS. For other organisms, I'm not sure. I'm guessing there are more applications but ghost-tree was designed with fungal diversity analysis in mind.