Darken unused Mask variables

Darken Mask variable inputs when Mask configuration dictates they will
not be used
Install - Uninstall structure update

Update scripts Install TMATS and Un-install TMATS to use loops for path
changes.

Update Install TMATS to print a message when Compiling code.

Update Uninstall TMATS to note that the user must remove startup.m file
changes for full uninstall completion.
Return to base director Run_exmple

Return to base directory after the Example is loaded with the Run
Examples script.

Added a cancel setup button.
Cleaned up the interface to allow for easier changing.

Changed order of examples flipping 2 and 3.
Clean up NR Equation Solv example

replaced all U references with X.

Added scopes and labels.
Remove Independent Initial Cond block

Remove Independent Initial Cond block and all places where it is used.

Also removed a few commented out lines that were missed during clean up.
dynamic plant clean up

Cleaned up a few name discrepancies in the dynamic plant model.
Merge pull request #32 from cheesie67/master

Pull in T-MATS cantera MATLAB version
Merge pull request #1 from GRC-RHC-Sim/master

Pull it