This would resolve issue #159 by the simple expedient of building a list of all the files in the staging directory, and using the sorted list to build the tar-ball.

Note this does not explicitly handle directories, thus any empty directory would be missing from the tar-ball. Since the Tool Shed uses hg internally this does not matter (same for git too).

e.g. silly test case showing the desired sorting:

$ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/venn_list && tar -tzf shed_upload.tar.gz
cp /tmp/tmpYAjHCW shed_upload.tar.gz
aaa
test-data/magic.pdf
test-data/rhodopsin_proteins.fasta
test-data/venn_list.tabular
test-dataAAA
tools/venn_list/README.rst
tools/venn_list/tool_dependencies.xml
tools/venn_list/venn_list.py
tools/venn_list/venn_list.xml
toolsAAA
zzz