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Makefile: Allow to launch a single functional test with valgrind by prefixing its name with valgrind_

This has no consequence since this rule is forced anyway.

Relative path is less robust when changing directory.

valgrind_should: valgrind on functional tests
valgrind_tests:  valgrind on unit tests

This invocation should also be more portable
See http://stackoverflow.com/questions/2792675/how-portable-is-mktemp1

Makefile: For tests ensure that vidjil is rebuilt with -O0 -g so that we get useful information with Valgrind (slower...)

Append some flags to CXXFLAGS
and use LDLIBS instead of LDFLAGS for -lm and -lz

See https://www.gnu.org/software/make/manual/html_node/Implicit-Variables.html

Now you must compile with make COVERAGE=1 to compile with coverage
information. There is another rule (called coverage) which compiles with
coverage options and then runs gcovr (if available).

The library is now built in core, where we have the list of dependencies
(dep.mk). Before dep.mk was in algo/ but the files it was refering to were in
core/. Thus the dep.mk file was useless.

	* 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