[bdg-utils-11] Adding testFile to SparkFunUtils

Fixes #11
Merge pull request #12 from tdanford/test-file

[bdg-utils-11] Adding testFile to SparkFunUtils
Added module-level .gitignore files.

This is mostly so that we ignore the src/main/resources/git.properties
file that's created by Maven during build, and reflects the
corresponding settings in the adam repository.
Adding the S3Test and NetworkConnected TestTags.

These are needed for some of the tests that will be added to the
bdg-utils-parquet test suites.
[bdg-utils-3] Migrating Parquet code out of ADAM

Changes in this commit:
* created the bdg-utils-parquet module
* added dependencies (parquet, AWS, Apache HTTPClient) which will be needed for this module
* moved over the contents of org.bdgenomics.adam.parquet_reimpl and io to this module.

The major exception to this last point are the index, RDD, and helper
classes from adam.parquet_reimpl which depend on ADAM-specific model
classes (like ReferenceRegion), in particular, RangeIndex, IDRangeIndex,
ReferenceFolder, and the RDD class which used the IDRangeIndex
specifically.