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should-to-tap.sh: dumps test + .log on stderr when a .should_get fails

This should ease debug when receiving mails from Jenkins.
vidjil.cpp: boolean out_segmented, similar to out_unsegmented

We will soon produce segmented.vdj.fa only when it is requested.
vidjil.cpp: output 'out/segmented.vdj.fa' only when the new option '-U' is set.

A very long time ago, 'out/segmented.vdj.fa' was considered to be
the main output of Vidjil, giving the (heuristic) segmentation of
each read. However, when many reads are segmented, writing this file
to the disk can slow the software (until 25%)... and this file
was used only to debug. By default, this file is now not produced.

The main output, with a summary of windows and representative, is in
'out/windows.fa', 'out/seq/clone.fa-' and now 'out/vidjil.data'.
algo.org: 'out/segmented.vdj.fa' and new option '-U'
Tests: update to latest IMGT
fuse.py: orders 'systems_segmented' according to GERMLINES_ORDER
builder.js: multi-germline menu with SystemBoxMenu
builder.js: multi-germline menu on two lines, starting from IGH
vidjil.less: systemBox (and systemBoxMenu) css bikeshedding
css: lessc
database.js : ssl check
database.js : use flash message instead of popup
server: apache install
database.js : ssl cert flag
database.js : rights function upgrade
database : permission >> in addition to the permission system to access patients each user have some specific right about creating new patient / uploading new files / scheduling runs