JCS cache configuration slightly changed.

MatrixWithHeaders has a multiplyWithConstants() function now
getCountsStranded() is now removed.
AlignmentModel is improved to handle stranded counts.
getCountsStranded() is now removed and getOverlappingReads() will return
stranded reads depending on the transcirption read of the alignment
model.
Function to return the scan statistic score as a double array added.
Bug in Scripture.connectDisconnectedTranscripts() is fixed.

ScriptureScorer is Scripture quantifier in the new code base. It can
only handle multiple files at this time.
StrandedCountScore & StrandedScanStatisticScore classes are removed.
Test class added to test JCS clean up.
Merging with repository.
Merge branch 'master' of https://github.com/mgarber/scriptureV2.git

Conflicts:
	.classpath
	.project