bug 23171 - move over libConsensusCore to build folder

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 124482]
bug 22690

add a 'dynamic scoreDiff' mechanism that increases the band-width when there is poor agreement between the read and template.  Helps the initial band track the correct alignment when there are large indels.  Also pipe out a few diagnostic value to see many matrix entries are being filled and how many flip-flops needed.

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 124515]
bug 22690 - factor out dynamicScoreDiff parameters into BandingOption.  Using the exsiting constructor turns off dynamicScoreDiff.  Add a new constructor that lets you set those parameters

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 124547]
stupid mistake in flip-flop -- fixes all cram tests bug 22690

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 124556]
Sketch of diploid support

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 124586]
       For csharp build, add .cs file

       [Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 124587]
consensus: bug 23171: enabling ConsensusTools build

Enabling the build of ConsensusTools, now that we have the mono_fsharp
and swig prebuilts available to us.

After these changes, we expect calling "analysis/bin/ConsensusTools.sh
--help" in the build output will produce the expected usage message.

Changes include:

  * Calling "make install" in ConsensusTools from assembly/Makefile
  * Add mono-install target in assembly/third-party/Makefile, which
    basically copies the mono prebuilts for the target os to the 
    redist output directory.
  * Change the path for mono in the ConsensusTools.sh script that 
    ends up in analysis/bin.  Now points to correct path to the new
    mono install in the redist output dir.
  * Modify ConsensusTools/Makefile to specify the path to the
    prebuilt.out/mono_fsharp version of xbuild.  Also specified the
    ConsensusTools.sln file as an argument to make it less ambiguous.
    Also added 'mkdir -p' of analysis/bin (for debugging when it
    doesn't exist yet).  Also removed all the unnecessary variables
    that were being exported.
  * Removed System.Data references in PacBio.Align.csproj. They are
    not used and our version of mono has them trimmed out.
  * Specify the path to bin/fsharpc for the F# compiler in 
    PacBio.StringTools.fsproj, because it will try to execute the 
    fsc.ext PE assembly directly (which doesn't work on all systems,
    such as ubuntu-0804).
  * Point csharp-pacbio target to our new version of swig in CSHarp.mk
  * Point Config-linux.mk at new version of swig (even though it is
    not really used in building Consensus).

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 124677]
consensus: bug 23171: removing references to dotnet v3.5

A couple of our .csproj file contained references to v3.5 of dotnet,
but we expect to use v4.5 for everything we build. 

This setting in PacBio.Analysis.ConsensusCoreManaged.csproj is the
biggest troublemaker:	

  <TargetFrameworkVersion>v3.5</TargetFrameworkVersion>

That actually forces xbuild to fire off a different compiler (gmcs) 
instead of mcs (underneath, gmcs is just "mcs -sdk:2", forcing it 
to use dotnet 2.0 assemblies).  

But our mono_fsharp prebuilt.out install has all the 2.0 assemblies
trimmed out, so it probably builds with 4.0/4.5 anyway.  But we should
make sure all our .csproj files are consistent, so that they at least
fire up the same compiler.

Also removed some other suspect settings (which didn't seem to make 
a difference in the compile), such as:

  <Reference Include="System.Core">
      <RequiredTargetFramework>3.5</RequiredTargetFramework>
  </Reference>

  <OldToolsVersion>3.5</OldToolsVersion>

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 124678]
consensus: bug 23171: reverting Config-linux.mk change

This file is shared between projects and the changes to enable 
a new version of swig were not compatible with all builds.  I think
this change might not have been necessary for the smrtanalysis
build anyway.

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 124691]
consensus: bug 23171: add "if linux" to CSharp.mk

Make sure to only run the os detection shell command if we are
running under linux to avoid error on other oses that may be using
CSharp.mk.  This still assumes that the csharp-pacbio target is only
used by the smrtanalysis build (not completely sure that is a valid
assumption though).

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 124692]
Add analytics link

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 124760]
Add ignore rules

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 124761]
Fix analytics link

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 124762]