Edit readFluxes and README.

 * Now readFluxes does not take any input parameters.
 * Edit the PETSc installation part of the README.
 * Update to PETSc v3.5.0.
 * Specify custom MPI directory and BLAS and LAPACK installations.
 * Add line breaks.
Add doxygen documentation.
Improve plotting scripts.

 * Add titles to plots generated by plot.py.
 * Add command line option for stride in plot2d.py and plot3d.py.
 * Write only nodes separated by the stride interval in the VTK files.
 * Add comments to plot2d.py and plot3d.py.
 * Bug fix: Correct array size for the y and z node coordinates.
Add 3-D case cylinder/Re250.

 * Remove 3-D case cylinder/Re200.
 * Remove "type: flow" from 2-D cylinder/Re40 input file.