Now the clusters are not output on stdout.

The clusters computed by cluster-junctions.cpp are meant to be visualized in the browser,
and do not influence anymore the main output of vidjil.cpp: one clone = one window.
This brings a great simplification in the code: a clone is now a 'junction' and not a 'list <junction>'.

Now 'detailed_cluster_analysis' only controls whether a representative is computed or not.

Again, this breaks some unit tests.

Now the MultiGermline contains only one germline.
The 'should' tests are still passing, but some unit tests are now broken.

Objects for the upcoming multi-germline heuristics.

Removes a large chunck of old useless code.
This was used to align sequences, but we do not use anymore clustalw here.

Clean the code, reorganizing output files

See http://leandroardissone.com/post/19690882654/nginx-405-not-allowed

d3js updated
jquery updated (use jquery 2)
jquery.form updated
jspdf updated
canvg removed (never used)
less.js removed (we don't compil css in the browser anymore)

Corrects a bug where nothing opens.

Conflicts:
	server/web2py/applications/vidjil/controllers/default.py

debug: original name order