root dir change for snakebids 0.4.0

[akhanf]

This PR is related to refactoring proposed in #123.

It changes output folder structure to prepend results/ folder when in workflow mode (run with snakemake), and not prepend results/ folder when in bids-app mode (run with hippunfold CLI)

In addition to this change, outputs are now placed in hippunfold and work folders, which are siblings (analogous to results and work from before).

These changes mean that when run in workflow mode, all the outputs are in results/hippunfold and results/work (ie according to snakemake best practices to not crowd the snakemake root folder), and when run in bids-app mode, all outputs are in hippunfold and work.

Note: more substantial refactoring could be done in later PR(s), where we can:

1. Add more subdirectories for organizing outputs (siblings to seg, surf, anat), like coords and xfm
2. Use the temp() directive throughout the workflow instead of using a separate work path. This would mean we could drop the copy_to_results rule, and instead of --keep_work can use the snakemake --notemp option to keep the temporary files

[akhanf]

This PR now also changes the way we dry-run test the workflow, putting the tests in the github workflow instead of a separate python file and pytest. Did this because of some incompatibilities with the way we were testing and snakebids, but it should make adding new dry-run tests much easier..