Optional parameters

This is an implementation of #137. 

I have removed some default parameters from the usual test case YAML files as well. Makes them easier to maintain and simpler to use. 

@pdraper Are there any default settings we should use for domain decomposition ?

See merge request !175

Formatting

"Fix" to #167. Added a script to run clang-format-3.8 with the appropriate style file. Is the 'Google' style with one modification: one can have an empty line at the start of a block. 

All the includes are now in alphabetical order without creating any compilation issues any more.

See merge request !174

Parameter file in snapshot

Sorry @pdraper.... one more for you...

This is an implementation of #140. The parameter file key-value pairs are written to the snapshots. 
Changes are:
 - Write the parameters to the snapshot.
 - Reduce the size of the parameter file structure by changing the maximal amount of lines it can contain.
 - Added an error message for when this limit is reached.
 - Change the type `lock_type` to `swift_lock_type` in `lock.h`

This last change is because `lock_type` is used in some MPI function prototype and our "#define" interferes with some of the includes if you are not careful about ordering. That solves the problem by naming the lock type in a unique way.

Apologies for the rather large changelog that this generates for 5 actual lines of useful code... 

See merge request !173

Conflicts:
	src/engine.c

fixdt kick changes.

Fixed the minimal SPH hydro version

Fix to #148. The code now runs without segfaulting when using the minimal SPH hydro code. Results are not great (by design) as the model is really poor (but simple).

Changes are:
 - A missing initialisation in `engine_init_particles()`.
 - A mistake in the calculation of the du/dt term.

See merge request !169

Kick task for fixdt and proper treatment of conserved quantities

This fixes #146 and #103.

 - In brief this adds a new task "kick_fixdt" for the case where we run with this policy. 
 - We then construct the type of kick task corresponding to this policy.
 - Some of the physics operations have been moved to separate files "drift.h", "kick.h" and "timestep.h" to simplify things and prevent redundancies.
 - Energy statistics are now computed at the end of the drift (and not of the kick any more) which allows to get a value even in a time-step not involving all particles. 
 - The frequency of the statistics is specified in the parameter file.

See merge request !167