Can now read cal files on command line.

- I made it so we can read cal files off the command line. Putting a cal file on the command line when reading in a root file now has a priority
- If only a root file is put on the command line, the cal info from the tree is read.
- If an analysis tree is read in, it's cal info supersedes any fragment tree info and the last input analysis tree has it's cal info read.
- If a cal file is read on the command line, the very first cal file on the command line is the overall winner of cal info reading. 
- This may be confusing so if anyone has any suggestions for a better order please let me know, I just went with what was already going on. Also I only performed very basic testing (does it read a cal file, does it read the fragment tree, etc.) so if this breaks anything for anyone please let me know the issue with details and I will fix it as soon as I can.