New simple unit tests for libbwa
Update installation docs
Update property name equivalency
Remove instruction on how to install pydoop
Add bcl2qseq
Update common program usage

Updated for new command line interface (one 'seal' command with
subcommands).  Also removed suggestions about data having to be on HDFS
and added some examples for dealing with various file system scenarios.
Updated for new prq command line interface and properties
Update for new seqal command line interface
Fix documentation about how seqal marks duplicates