Merge pull request #33 from BillMills/master

tiny testing bug
fixed options setting if filename not specified.
now loops over multiple run.mid files given on the command line
Merge remote branch 'upstream/master'
Merge pull request #34 from pcbend/master

fixed options and updated multi mid file reading.
reorganized TAnalysis dir under libraries in preperation to add more SHARC classes.
Added comments and most the functionality to do analysis on the fragment.root file in the program.
Merge pull request #37 from pcbend/master

Add comments and most the functionality for fragment.root analysis with in program.
- Adding missing makefiles to /libraries/TAnalysis/ subfolders
Merge pull request #38 from carlu/master

- Adding missing makefiles to /libraries/TAnalysis/ subfolders
Merge remote branch 'upstream/master'
skeleton grsirc and grsi_logon are included and working.
Merge pull request #39 from pcbend/master

new grsirc and grsi_logon files included to allow for some new features coming down the line.
Added formated out put to the calibration manager.
Added root dictionaty for XmlOdb.
Added the ability to print a correctly formatted .cal file to either stdout or a passed file name.
Merge pull request #40 from pcbend/master

Add some calibration functionality
 'Fixed' a bug that caused a std::bad_alloc error when sorting large (<2GB) files.
Merge pull request #41 from pcbend/master

 'Fixed' a bug that caused a std::bad_alloc error when sorting large files
Added Sharc analysis class files/directories/lib