In _chemfigity.py if dest_dir is null, then the directory is the same
as tex_file. If both null, then the directory is the
execution directory (pwd).

In settings.yml, added text_depth setting to chefigit
configuration which specifies how deep to look into dest_dir
if tex_file is null.  Updated help strings in settings.yml

Updated settings.yml to reflect -t template.

Added version to phyles dependency (0.2.9).

Newest version is 0.1.3.