Large re-organisation of the package to make it more coherent.

- packages similar to tasks or instruments should implement the manager and everything related to it in a manager package and put the base modules at the root (see tasks).
- preferences, state plugin now have their own packages in utils.
- log_system is now under utils as log
- the starting_log command now takes an optional arg to prevent capturing stdout and stderr, the -s commandline argument can be used to start in this mode.
- dependencies previously administered from the task manager now have their own plugin under utils/dependencies.
Minor fixes.
Fix LoopTaskView.
Fix editor selection after loading a measure.