change makeflow bundle directory output format

This is the start of the workflow linker.

__Overview__

In this set of changes the linker extracts the dependencies from
Makeflow and Python files.

The linker starts with a Makeflow workflow description and recursively
traverses the dependency tree. Once all of the dependencies are found
the linker creates a packaged version of the original workflow. This
packaged version contains all of the necessary files to run
successfully.
output new makeflow file relative to bundle directory
remove unneeded output from makeflow bundling
return a copy of the filename, otherwise all files end up with the same name
use fatal instead of exit
fix broken makeflow_linker* tests
scaffolding for linker
call makeflow from linker
redirect stdout from makeflow process to pipe
process makeflow output character by character
outline for determining driver
fill in details of dependency struct
display dependencies
store file type in dependency structure
basic structure for finding dependencies.

Still need to fill in the gaps for the actual python script.
But it should be easy to strip the necessary pieces out of the other linkers
initial python driver
parse output of python driver
add dependencies of makeflow dependencies to list
compute depth for dependencies
set parent and recursively search tree of dependencies