GX Pipeline should output into its own folder + include the config file

[davidmummy]

Instead of writing the output to the same folder as the data, the GX pipeline should write its output to a folder called "gx". This is analogous to the spectroscopy functionality for output files and will make it easier to align with our new folder structure standard.

Further, it should copy over the config file used to create the output, so that future users can (1) know what parameters were used and (2) easily re-run it themselves if needed.

[davidmummy]

Assigning this to @Sarahhongqin to work at her convenience -- no rush. @Sarahhongqin please get help from @annacostelle or @sl609 as you need it, and comment here or on slack if there is anything unclear about the requirements.