updated Dev parameter files

[evazlimen]

Updated the parameter files with the dev branch so that they can be run without modification.

• For 1D tests, added y and z boundary conditions =0. For 2D tests, added z boundary conditions =0.
• Changed all default output directories to the current directory.
• Changed the domain of Shu_Osher.txt to [-1,1].
• Changed the noh_1D.txt initial condition name to Riemann.
• Clarified within Ryu_and_Jones_1a.txt that the parameter file is for shock tube 1a and not 4d.