Update obsolete variable names left in codebase

[clmould]

Some obsolete variables from the renaming work are still in some files, eg in the examples/data folder, and in some mfiles in the test suite. These need updating to their new variable names.

For the MFILEs in the examples/data dir, I just used the copy of process input at the end of the mfile along with the update_obsolete option to run process and update. Had to remove some leftover ixc=52, and some ixc=13 if ixc=140 is also in use (as done in #3662)

[clmould]

I will update the MFILEs in the examples/data dir. to remove obsolete variables from them. @timothy-nunn and I will look into generating mfiles from an eval in.dat when they're needed in the example notebooks instead of storing loads of mfiles in the examples folder. The test assets with obsolete variable names in them will be sorted in #3952