Halo finder

[nataraj2]

In this PR

1. parameters halo_component_threshold and halo_extrema_threshold are now being read in, and passed into Reeber.
2. includes changes to Reeber required for the halo finder. ie. changes to Util/reeber/src/reeber.cpp. Ideally, Reeber should be a git submodule, which will be done in a later PR.
3. An example of the halo finder for dark matter particle simulations is in Exec/HaloFinder. Note that the IC file list should be supplied through a text file specified in the inputs with the variable nyx.binary_particle_file.
4. VTK files are written for visualization of the halo particles. Simple binary files are written as well. Source/IO/Nyx_output.cpp has the routines.
5. Lightcone shells and halo output files are written into a directory Output. Output is turned off by default. Options are provided in the inputs to write the output - nyx.write_lightcones_and_halos_vtk and nyx.write_lightcones_and_halos_simplebinary
6. Python scripts - Read_SimpleBinary_Halos.py and Read_SimpleBinaryLightcones.py are included in Exec/HaloFinder - this can read the simple binary file output for halos and lightcones.

Attached images show the lightcone shells (gray) and halo locations within the shell (red) at z=5.59 and z=0.99 for a 128x128x128 mesh size run, with halo_comp_threshold=3.0 and halo_extrema_threshold=8.0 (just for testing). The domain box is shown as well.