Merge tag 'v0.0.2'

Updated maint-0.0 to work with target machines.

a) Support for edison, hopper, mira, and titan was updated and tested on all
systems.  This required specifying more recent compiler versions and flags (and
other system software), modifications to the file system paths, and some code
changes to work around compiler issues.

b) Additional performance timers were introduced, and some were also deleted,
to better capture performance of the model. The timing library was also
updated, and then modified so that it does not interfere with other performance
tools. Finally, some additional provenance (e.g. git describe output and
SourceMods subdirectory) is now archived with the performance data.

c) Some new performance optimization options were introduced into POP and CICE.

The current maint-0.0 does not work on the target systems. After doing the
minimal updates (updates to paths in config_machines.xml; updates to support
new file system structures in create_newcase and config_definition.xml; update
to loaded modules on titan (the test system) in env_mach_specific.titan;
deleting unnecessary files with coding errors: drv_input_data.F90,
offline_driver.F90, unit_driver.F90; introducing workaround for PGI issue in
thread_mod.F90), the changes from maint-0.0 to this branch are BFB.

BFB was tested only on Titan using the PGI compiler and for only one case. This
was a fully coupled run and both MPI-only and MPI/OpenMP large runs were BFB
based on the component logs out to 5 simulated days.

* tag 'v0.0.2':
  Augmenting capture of .git or .svn provenance.
  Modifying the timing library so that it will not conflict with VampirTrace [from B. Jamroz]
  Adding capture of SourceMods and .git or .svn provenance.
  Modifying compiler specification for Edison, required for this version of MCT.
  Modifying compiler specification for Mira, required for this version of CESM.
  Updating performance data archive logic, including system-specific paths.
  Updating system software versions for Bluewaters, Edison, Hopper, Mira, and Titan.
  Removing files in chemistry utils that are not used (and some of which are buggy).
  Introducing error checking logic in CICE sea ice component.
  Adding additional performance optimization options in CICE sea ice component.
  Modifying performance instrumentation in CICE sea ice component.
  Fine tuning (and cleaning up) performance instrumentation in driver.
  Adding additional performance optimization options in POP2 ocean component.
  Cleaning up code in the POP2 ocean component.
  Modifying performance instrumentation in spectral element atmosphere dynamical core.
  Introducing work around in the spectral element atmosphere dynamical core for compiler issue.