Update .gitignore

added MAIZSIM graphics files to the ignore list (they are too large)
updated documentation

Signed-off-by: Dennis Timlin <Dennis.timlin@ars.usda.gov>
modified files to simplify input structure

removed three input files and distributed parameters to other files
Modified input file structure and reading

I modified the input file structure to use less files. The input data
are not distributed more consistently among the modules
These are the input files for one simulation

These are input files for a site in Delaware that was used in our paper
Made a few modifications in run file

Run file looks for input files in Y: drive. Also added several batch
files used to copy executable and dll to working folder
Update README.md
removing extraneous files
committing exe file
Merge branch 'master' into port
Need one more byte for NULL, but still looks quite dangerous
Fix line-break handling for detecting input file names
Ignore Mac/Unix object files