Remove remaining vestige of old Score API

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130448]
Collapse PBFeatures into Features

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130449]
Introduce new "Read" class

Read class holds read data as well as metadata: read name, information
about the chemistry condition

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130450]
MultiReadMutationScorer now needs a dictionary of configs by chemistry name

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130451]
Fix SWIG build

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130452]
Version 0.7.6

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130453]
Work around SWIG glitch

SWIG now seems to be incorrectly deciding that MultiReadMutationScorer
is an abstract class, so we have to tell it otherwise

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130454]
Get SWIG to recognize the map type

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130455]
Copy constructor for MappedRead

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130456]
Fix C# build

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130462]
Fix ConsensusTools build to accomodate updates to ConsensusCore
bug 23893

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130470]
Fix Edna to accommodate updates to ConsensusCore, and purge PacBio.Analysis namespace.
bug 23893

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130472]
Silence some warnings, reinstate LD_LIBRARY_PATH-fu with MJ's helpful suggestions
bug 23893

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130528]
Continue banishing spectre of Primary Analysis
bug 23893

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130529]
The new QuiverConfigTable abstraction left the memory management of the QuiverConfig in the hands of whomever created the QuiverConfigTable, this solves that using value semantics
bug 24640

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130841]
Simplify interface between ConsensusCore and ConsensusTools, revive old Score() interface
bug 24640

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130867]
Fix ConsensusCore test

[Bug 24663]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 131137]
On OS X, use clang++ by name, but use the GNU libstdc++ (libc++ doesn't work with SWIG yet)

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 131144]
homebrew boost location

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 131145]
Fix lint

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 131146]