Change around logic for creating time files

[mandli]

Basically move the creation of the 'timing.csv' files to amr*.f90. Also removes the 1D code from the 2D stuff given that we have an explicit 1D code now (supercedes #223).

[rjleveque]

This seems fine. It still gives some garbage at the first output time when doing a restart, but that's not so easy to fix and at least all the timing data is preserved and the user can edit timing.csv to clean it up if desired.