Initial commit of dvm-dos-tem

Compiles and runs a single site on aeshna.
Adding a doxygen file

.gitignore ignores docs/*
Swapping to a much simpler Makefile

This file needs to be hand updated, but is <200 lines as opposed to the previous one at over 1300 lines.
Merge branch 'docs-and-make'
Removed eclipse specific config files.
Updating the readme.
Update README.md
Fixes to Makefile for fresh clone errors, fix to PI check
Merge pull request #1 from alecbennett/master

Updates to dvm-dos-tem
Merge remote-tracking branch 'uasnap-MAIN/master'
Merge pull request #2 from tobeycarman/048ac859

Remove eclipse specific files, update readme.
trivial update to README.md
Rename a bunch of files.

Move stuff to a new horizon directory, rename
error code header.
Delete the status outputer files.
Modify makefile to reflect file changes.
Changes to let dvm-dos-tem run in "spatial series" rather than "time series".

Notes from Fengming Yuan, 6/29/2012
---------------------------------------

Added 2 running subroutines in Runner.cpp, runmode2 and runmode3.
	- runmode2 is for timeseries,
	- runmode3 is spatial series.
The idea is that let the TEM run through a loop of 'cohort' (cell) at
 monthly time step. At the end of each time step, save all needed states
variables into the so-called 'restart' file. When starting the next time
step, the model will first read the initial conditions from that
'restart' file to continue with.

BUG: the restart file after each time-step is not output correctly.

There is one big changes in the code with regarding to the input data reading.
 Previously I let the 'cohort' (cell) ID to be searched throughout the input
.nc files each time – looks like that will cost a lot of time. Now the codes
in this aspect have changed so that in the beginning all 'cohort' (cell) ID
are read into a few vectors, and then data-reading can directly go into
the .nc files – no more searching (although it needs a little bit more memory).
Merge remote-tracking branch 'upstream/master'
Merge pull request #3 from tobeycarman/master

get the ua-snap up to date with tobey's master
Change to SITERUN, add comment.

Trying to run the model with the old test dataset
for one location.
Doxygen comments to Runner class.