[ADAM-322] Adding ADAMFeatureField for projections over ADAMFeature.

For some reason, we'd neglected to include an ADAMFeatureField class in the adam.projections
package!  This commit fixes that.
[ADAM-307] Fixing Features2ADAM so that it can be run from the CLI.

Features2ADAM fails because it doesn't include an 'index' field in its
second command-line argument, and therefore Args4j can't parse the Features2ADAMArgs
object off a command line.

This commit adds the missing 'index' argument to the Features2ADAMArgs class.

There is a test for this additional feature -- however, that test is marked as IGNORE
because we can't get it to work either locally or on Jenkins.  This should be addressed,
and I'll open up a ticket for it.  In the meantime, however, we've verified that manually
that this patch works as advertised.

Also modified PrintADAM to use the scala.Console.out rather than System.out.
This seems to allow us to (in tests) redirect the output stream using the
Console.withOut command.
Merge pull request #308 from genomebridge/features2adam-bug

Fixing the 'index 0' bug in features2adam
Upgrading the version of bdg-formats to 0.1.2-SNAPSHOT in the pom.xml
Automated refactoring, renaming all the classes to drop the ADAM prefix.
Starting to fix the field names on Variant and Record types.

In particular, making the following changes:
* updating the (deprecated) uses of Record.end to Record.getEnd
* changing Variant.get/setPosition to Variant.get/setStart
* changing Variant.get/setVariantAllele to Variant.get/setAlterateAllele

The tests still aren't passing, this is mostly due to Indel realignment tests
and I'm not sure why they're not working.  @fnothaft, can you help out a bit here?
Fixing the remaining Variant and Read naming changes, that happened when I rebased.