Added patient and run names as well as usernames in log views

Moved software and parameters to the end of the sample log

There was an inconsistency in the specification: "stop" was used several times, and "end" once.

We should follow format-analysis.org specification: "Positions on the sequence start at 1."
Note that these tests were introduced in 745b47db (Feb 2016), but, at this time, we did not check these positions.

Resolved an issue where samples would not be displayed in the global
compare view if the sequence file involved was present in multiple
sample_sets (patient + run)

Resolved an issue where attempting to remove a file from a patient or
run which was attached to a patient or run that was previously deleted
could cause a server error when checking permissions

Resolved some issues with the new queries which would systematically
cause a server error

This allows to know where we come from and therefore where we must redirect to.

It was not provided to the file/edit.html view which needs them to display
help on each pre-process.

This two views (file/add.html and file/edit.html) should definitely be
merged. The form has been renamed as for file/add.html.

Fix 6d28e261

Added button to compare sample_set view in run list

Fixed an issue where runs did not appear in the compare sample view and
one could not compare samples of a run

On some browser (at least Chrome 42) this may totally fail the filter()
function which breaks the autocomplete feature.

This is some documentation on how groups and users work inside the
permissions system. It also includes a procedure to follow when creating
an organisation with multiple roles

Fixed an issue with the calculation of associated_id when deleting
sequence files.

Added some packaging documentation.
It contains instructions to create a debian standards compliant package
of a vidjil release version (so only the algorithm part)

Added some carriage returns to showLog in order to make the js logs
easier to read

This commit resolves an issue with the info container, and more
specifically the locus line where if no clones/loci were detected in the
sample, then a Node Object would not be instantiated and therefore would
crash when trying to append it to the interface

When zooming a lot, the labels overlap the clones.  We shift them a little to
avoid that (but this may look weird when not zoomed in).

This was not very straightforward.
Pointed out by @rchikhi.

Added indicator when ajax query is in progress

First load read permissions and set all read accessible elements to
false for the requested permission.
This helps because initially only True permissions were loaded which
lead to a very slow patient list controller and many database queries
when a non-existant permission was loaded and then requested multiple
times

Moved log menu entry into section visible to all users