Move FATES phenology to be self-contained

Merge branch 'ckoven/phenology_internal'

replace externally-dependant phenology into FATES internal code

FATES phenology was going through the interface so that it could
leverage CLM's time-accumulation infrastructure to track growing
degree days. This was deemed overkill and so instead GDD are now
tracked at the FATES site level and kept internal to FATES. Also
changes the definition of GDD to be based on daily mean temperatures,
which allows both the structural simplicity of calculating GDD at
daily timestep, and gives the correct definition of GDD. However this
requires it to be answer-changing with respect to the old code.

Fixes: #63

User interface changes?: No

Code review: ckoven, discussed changes with @rgknox and @rosiealice.

Test suite: ed - lawrencium intel; yellowstone gnu, intel, pgi

Test baseline: 1fc6811 - Should in principle be answer-changing. In
practice tests were bit for bit with baseline. These changes probably
do not have adequate test coverage.

Test namelist changes: none
Test answer changes: climate changing

Test summary: expected failures #14 f09 and f19 restart. #43 f10 gnu
restart on yellowstone.