Add default tool dependencies directory to .hgignore.
Add tools_directory to setup response (in case client wants it).
Use objects instead of tuples to represent staging actions.

Should help readability.
Add inputs_directory to setup job config dict.
Enhance client to work without path rewriting.

Add option to stager to not attempt to rewrite input, output, and config file paths. Add path mapper to allow an LWR client to build expected paths before transferring files. These options together enable the LWR Galaxy client to be tweaked to build job inputs (command-line and config files) with the correct remote paths instead of building the inputs and then rewritting them.