Init branch fabian

* Added .gitignore file on project root and in node layer
* Fixed wrong file mode bits -> 755's to 644's
Adding Sod shock tube test case (Test_SOD.h)

Generalization for arbitrary initial condition

IC can be specified on command line:

    * Location of initial discontinuity (0 <= x <= 1) : -x0
    * Density left/right                              : -rho1 / -rho2
    * Velocity left/right                             : -u1 / -u2
    * Pressure left/right                             : -p1 / -p2
    * Gamma left/right                                : -g1 / -g2
    * Correction pressure left/right                  : -pc1 / -pc2

Moreover, filled channel 7 and 8 of StreamerDummy_HDF5 (Types.h) with total
energy and specific internal energy, respectively.
Implementation of HLLC flux

* Adding method _char_vel_star(...) to compute the wavespeed of the
  intermediate according to [1].

* Computation of the RHS term for the advection equations according to [2].

* Fixed boundary condition in Test_SOD.h to all boundaries absorbing.

The flux implementation was tested individually in all 3 dimensions using test
case 6 and 7 of Section 10.8 in [3].  Each individual flux test generates an
identical result.

[1] P. Batten, N. Clarke, C. Lambert and D. M. Causon, "On The Choice of
Wavespeeds for the HLLC Riemann Solver", SIAM J. Sci. Comput., Vol. 18, No. 6,
pp. 1553--1570, 1997

[2] E. Johnsen and T. Colonius, "Implementation of WENO Schemes in Compressible
Multicomponent Flow Problems", Journal of Computational Physics, 2006

[3] E. F. Toro, "Riemann Solvers and Numerical Methods for Fluid Dynamics",
Springer, 2009, 3rd edition
Merge branch 'fabian' of github.com:fab4100/CUBISM-MPCF into fabian