Assumptions on filenames and directory structure

[dshean]

Not everyone will run the dg_mosaic workflow, which creates the r100.tif/xml files. Hopefully not a requirement that these are available.
We should probably mirror the ASP CLI here as much as possible, so --bundle-adjust-prefix instead of --bundle_adjust_directory. I realize some of the ASP CLI options are not consistent across tools, like the reference DEM argument in bundle_adjust and stereo.
In the user-defined variables, do the ba_directory and stereo_directory strings require trailing slashes (as in example). Maybe have logic to strip trailing slashes, when constructing standard paths to specific files.