Fixed pass vs. not implemented error.

bug 21763

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 119766]
allowing python < 2.7 to get version first - Tracking bug 21562

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 119852]
Modify MJ's fix for version querying

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 119854]
Fix so that `start` returns the value of `run` to pass along to sys.exit.

bug 22579 

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 119898]
Makefile work

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 120019]
Add new FastaTable and ReferenceTable classes.

The ReferenceTable provides a very convenient way to access all
reference contigs by local identifier (cmpH5 ref id, for instance).

I've decided to rename CmpH5Reader::referenceTable to
CmpH5Reader::referenceInfoTable to avoid confusion with the
ReferenceTable class.  This will require updating tool code.

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 120020]