Avoid redundancy in error messages.
Reworking of version checking.

Adds missing checks to the 'java' command (JRE), and to GATK. Improved version
reporting and error messages. Adds unit-tests for the versions module.
Ensure pipes passed to commands are closed.

This ensures that the processes recieve SIGPIPE if the pipes are broken.
Move version info to root __init__.py file.
Function to add multiple command-line values.
Do not import Pypeline class in root __init__.py
Updating manifest.
Updating pylint, warn on missing doc-string, etc.
Initial step in general 'paleomix' command.

Add a 'paleomix' executable, which acts as wrapper around other scrips
included in the PALEOMIX distribution. Ultimately, this script is to become
the main interface for interacting with PALEOMIX tools.
Add filtering to BAM regions iterator.
Fix for coverage/depths with regions.
Merge 'bam_duphist' into 'paleomix' commmand.
Wrap BAM tools in 'paleomix' command.
Wrap pipelines in 'paleomix' command.
Wrap final commands.
Fix bug in node-building when Padding = 0.
Update help string.
Various improvements to makefiles/parsing.
Add a few missing tests.
Fix regression caused by fix to Padding: 0 handling