Cleaned up comments and documentation in forceFindBestBarcode

Cleaned up comments and documentation in parseReadIntoTagAndTaxa(String,
String, boolean, int, int)[overloaded version]

Cleaned up comments, debugging, and docs in forceParseReadIntoTagAndTaxa
Comments on the reason the overloaded constructor with the
paddedSequence was important and where it was used.
Removed all debugging elements

Added comments and documentation on all added methods and logic
structures

Explained variables where it may not be obvious why they exist or where
they are declared.

Added and / or modified the following methods.  Methods are all private.
excludeTagCount
combineTBT
sumIDs
logIds
printTagCountMap
printTagsAndTaxaByLane
processParisCounted
checkForPairs
resetTime
reportTime
parseFlagArgs (modified from Nic Kiely's parseKeyFileList)