Update cmp.h5 file primary version from 1.3.1.SF to 2.0.0.
bug 24731

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 135560]
Revert blasr's default maximum interval finding to 'classic-mode', 
add an option '-fastMaxInterval' to enable fast maximum interval finding.

With '-fastMaxInterval' option turned on, blasr no longer searches for
max intervals exhaustively, and is a lot faster (usually 10 times) in 
finding alignment candidates. However, occationally, blasr may return 
alignments which are slightly different from the optimal.
bug 25290	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 135710]
Update changelist and blasr.t.
bug 25290

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 135716]
Add an experimental option "-aggressiveIntervalCut". When this option is 
turned on, blasr aggressively filters out 'non-promising' candidate intervals
if there exists 'promising' candidate intervals, whose PValues are much  
better than the remaining. 
With this option, blasr is likely to ignore short alignments of ALU elements.
bug 25302

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 135736]