added flowcell:lane variable.  All possible flowcell lane combinations
from input directory are set to this variable
Added lane information and formatting for Summary_Stats.txt logging and
output

Added output formatting for final Tags_By_Taxa.txt.  Using
addEmptyLanesToTBT all possible flowcells and lanes are listed next tag.
 If there was no tag count for that lane, the is a zero inserted.  This
keeps the final output formatting consistent for post-program parsing.
no changes made
Made some content changes
Detailed install and execute instructions
Added Amazon EC2 setup script
Ross's edits incorporated
newest jar 2013-02-21