Remove "||true" from Makefile, so that an error code will be returned 
when blasr fails to compile.
Change common.mk so that blasr is no longer compiled statically by default. 
In order to compile blasr statically, 'STATIC' needs to be overwritten.
bug 25263

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 135994]
bug 25263 - keep using -static in the build

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 136013]
Delete duplicated header files (Alignment.h and AlignmentStat.h exist in 
both common/algorithms/alignment/ and common/datastructures/alignment/)
bug 23801

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 136133]
Add an option noFastSDP to blasr. When -noFastSDP is specified, blasr
will not use fast heuristic algorithm (graph paper) to speed up 
SDP.
bug 25328	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 136215]
Disable -noFastSDP, enable -fastSDP, and switch blasr's behaviour back
to 'classic' mode.
bug 25328	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 136223]
bug 23801 - restore cpp/alignment binaries except old blasr

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 136704]
bug 23801 - submitted the unchecked modification

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 136713]
Add a cram test for unrolled resequencing.
bug 25328	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 136786]
bug 25426 - globally serarch ThirdParty and replace

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 138463]
bug 25021 - remove one warning from the cpp Makefiles

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 138477]
Update blasr description of maxAnchorsPerPosition.
bug 25105	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 138628]
Prop change 140182 to legacy blasr in case MC needs it.
bug 25302	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 140298]
When -concordant is turned on, use the 'typical' full-pass subread 
instead of the 'longest' full-pass subread as template for concordant
mapping.
bug 25186

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 140413]
Update MappingParameters.h, change math to cmath.
bug 25186

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 140415]
Bug 25737 - merge from pull request from the github, this solves 4.7 issue, but not 4.8

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 140465]
Prop change (140573) to legacy blasr.
bug 25737	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 140577]
Fix a bug which causes loadPulses compiled with gcc4.8 to fail.
bug 25744	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 140686]