Merge branch 'thesis'

Conflicts:
	doc/KH-hllc-plm-rk3.pdf
	doc/KH-hllc-plm-rk3.png
	doc/index.org
Set up a blobs problem (hijack KH for now)
Add a sequential HDF5 write option to the unigrid module
Give blobs problem a size parameter to zoom in on contact layer
Merge branch 'blobs'
Merge branch 'master' into gravity
Study collapse1d problem carefully to see where problems arise

This commit has debugging output in the block.c file, which allows to
plot the energy and momentum source term directly from the gravs and
gravp equations. There are two main findings:

1. The time step can be made small enough that the gravp equations get
   past the first time step, i.e. they do not add too much momentum for
   the available energy. It will be useful to see whether the means of
   computing grad-phi has any impact on spurious momentum
   addition.

2. There is a bug with the boundary conditions: they are currently never
   set for phi and grad-phi.