Split the adam-commands module into adam-cli and adam-core

This commit bumps the version to 0.6.0.

The new dependency tree is linear -- 'adam-cli' depends on 'adam-core' depends
on 'adam-format'.

All CLI code is now found exclusively in the adam-cli module. There is no
longer any dependencies in adam-core for command-line parsing, etc.
The AdamMain class has been moved from adam.AdamMain to adam.cli.AdamMain.
The 'commands' package has been renamed to 'cli'.

The CompareAdam code has been split with the back-end code in adam-core and
the cli code in adam-cli.

Only the adam-cli module create a self-executing jar for use on the
commandline.

Aux files like the README and Jenkins tests have been updated.
Merge branch 'master' of https://github.com/bigdatagenomics/adam