Corrected couple of bugs and typos

[arango]

Several typos and bugs have been reported in the forum:

• Corrected misplaced END IF in routine set_avg.F. Many thanks to Hugo Bastos for reporting this ​typo.

• Added missing code in def_avg.F needed when restarting and writing time-averaged squared tracer. Many thanks to Wang Dakui for reporting this ​problem.

• Corrected problem when writing EcoSim logical switches into NetCDF files. They are now written as integers. I missed these switches when I changed all the logical flags in the I/O NetCDF files. Many thanks to Dmitry Tokarev for reporting this ​problem.

• Corrected typo in checkdefs.F when reporting CPP option UV_SMAGORINSKY. Many thanks to Kate Hedstrom for reporting this typo.