Improvements to LWR documentation.

Add separate examples for MQ driven stuff - this should clear up things and make it clear which new parameters are required when using message queue and which are no longer required. Add more documentation for remote dependency resolution. Document rewrite_parameters.
Ensure new_file_path exists before set_metadata.py generates metadata.

This directory is required to exist but usually unneeded because Galaxy creates this directory on startup. However, when setting metadata remotely with the LWR that remote Galaxy instance may have never been started and this directory may not exist.
Remove no longer valid log message.
Optimize/correct LWR remote metadata generation for working directory outputs.

Previously I was attempting to mimic Galaxy's behavior of copying these files to a fixed output location after execution on the remote server before setting metadata. This was an un-needed copy since it appears to easier to just send the metadata generation code the expected path on the working directory.