Refactor DbHelper::truncateAllTables() to truncate non-core tables, and tweaks to DatabaseTestCase tests.

Use an angularjs directive to create Piwik notifications. The old class still remains since notification placement is out of scope for the notification directive.

Fixes #6313 - When a user starts to get a User ID set, then we set this User ID to the existing visit rather than create a new visit for this user id specifically

Refs #6313 Adding test case showing the bug (it creates a new visit but we want this visit to be re-used)

Fixes #6314 do not display error Warning: shell_exec() [function.shell-exec]: Unable to execute 'stat -f -c "%T" /proc 2>/dev/null

Remove and deprecate Piwik::setUserHasSuperUserAccess() and switch to using Access::doAsSuperUser()

I noticed the example command was lacking a bit of documentation / help on how to continue after generating this command

Add _isPasswordHashed parameter to UsersManager.addUser (mirrors parameter in UsersManager.updateUser).

 improve readability of code

Conflicts:
	core/Tracker/Db/Mysqli.php

coding style fixes, some PHPStorm inspection fixes, improved readability of code, few refactorings, all as part of our code cleanup strategy

Removing disablePurge hack in tests, as this should not be needed anymore