Conflicts:
	examples/main.c
	src/engine.c
	src/engine.h

Use of threads as command-line option.

Made the number of threads a command-line parameter again.

I have restored the `-t` command-line parameter and removed the parameter from all the yaml files. I have also updated the run.sh scripts with a default value of 16. 

That fixes #144 and the branch can be removed if you are happy with the changes. Thanks !

See merge request !144

Root level parts

Handles the case when the top-level cell size increases so that
the cells need to be regenerated and particles re-attached.

The technique is to resample the old cell space and use the node
IDs to populate the new one. This should minimise the need for
particle movement, so should be a little less expensive than a 
full initial partition.

If the resample fails we fall back to a full initial partition.
Could be a better idea to use the same technique as in main.c,
but we don't do that.

Fix for issue #31

See merge request !112

Conflicts:
	examples/main.c
	src/const.h
	src/engine.c
	src/engine.h
	src/space.c
	src/units.c
	src/units.h

Conflicts:
	src/Makefile.am
	src/runner.c
	src/task.c
	src/task.h

size_t

Another batch of `size_t` fixes, i.e. replacing `int` counters over the particles by `size_t` to allow for more than 2G particles per rank.

There's no hurry for this, mainly cosmetics and future-proofing.

See merge request !137

 Conflicts:
	src/partition.h

Parameter handling imported from old main.c.

First version of main() using a parameter file to get constants.

That's pretty big but does not touch the physics, the parallelisation nor MPI.

In brief:
 - Latest version of the parser from @jwillis 
 - More uniform name of functions in the unit module.
 - Added the ability for the `engine`, `space`, `unit` and `partition` objects to construct themselves from a parsed parameter file.
 - Added an example yaml file with full documentation.
 - Added yaml files and run scripts for the Sedov, Sod and uniform examples. 
 - General tidying of the `main()`.
 - Dropped the dependency on z-lib which we don't use.
 - Updated the README to reflect the new command-line parameters.
 - Cleaned-up the `main()` such that the only command-line parameters read in are policies and debugging options. 
 - Added the option to do a 'dry run'. This reads the parameter file, allocates the memory required by the ICs but does not read anything and constructs a space and engine. This allows us to check the validity of a given parameter file.

Happy to guide you through the changes if need be. 

This closes #81.

See merge request !140