#32 Explain tool descriptor command environment better

[Jonathan Clark]

Tip: Use move instead of ln -s for input/output files (LoonyBin should use absolute paths)

Note that each vertex is run in a new, clean current directory.

Follow-up: is the current directory (where I can "carelessly write
out") also the execution directory for the tool? That is, if I write
out to "blah.conf" in the current directory can the next command be
"run-blah blah.conf"?

Also, how do Java classpaths interact with the path files? Or do you
add another layer of indirection, say, with a script that calls the
appropriate java class?

I guess in general I'm just having a tough time keeping track of all
the directories and symlinks that are created, and what needs to be
where. But I guess that's the toughest part of the job.