Fixes a couple of bugs caused by the previous changes.
Add PG tag to readgroup information.
Add extra status-messages during setup.
Various improvements to AtomicCmd.

- Allow execution to be carried out with CWD set to the
  current temporary folder.
- Add support for specifying executable files, as well as
  auxiliary files required by said executables (scripts,
  data-bases, etc.).
- Convert functions to classmethods when possible.
Simplify CLI options, and add ini-file support.

Merges the --gatk-jar and --picard-root parameters into a single
--jar-root parameter. Add support for setting (most) options in
either /etc/pypeline.conf or ~/.pypeline.conf.