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Implements affine gaps by storing three matrices, B, Bins and Bdel.

As the 'operation' struct now contains the score, the S table is useless.

Edit operations, with their score computation and their backtracking information,
are now defined in a unique location.
The code should thus be more flexible and easier to read and maintain.

The computer science department of the Université de Lille is is now CRIStAL

Previously we created small arrays of three integers to store information for backtracking.
Now we have a structure storing the same information so that we can allocate an array of structures.
Therefore we can allocate the whole array at once, and we don't need anymore to have plenty of allocations of three integers

That solves signed/unsigned compilation warnings.
This had no effect in practice but that makes the compiler happy.

	* Refactored main vidjil.cpp (core/windows.cpp, core/windowExtractor.cpp)
	* Removed unused html output
	* Better json output (core/json.cpp)
	* Updated main stdout, with representative sequence for each clone
	* Updated parameters for FineSegmenter (delta_max) and dynprog (substition cost)
	* Bugs closed

	* Better heuristic, segments more reads (core/segment.cpp)
	* Better and faster selection of representative read (vidjil.cpp, core/read_chooser.cpp)
	* Better display of reason of non-segmenting reads
	* New normalization against a standard (-Z) (core/labels.cpp)
	* New experimental lazy_msa multiple aligner
	* New .json output
	* New unit tests
	* Bugs closed

	* First public release