Subset-nwm-netcdf

1) Add a new flag "include_AA_tm12" to control whether to subset tm01 and tm02 files of analysis_assim configuration. Default is True

2) fix a bug in spatial query module: If incoming geometry is 3D, convert it to 2D before spatial query

1) Remove previously added "time" dimension in "reference_time" variable as it was a violation of CF convention on "coordinate variable"";
see: http://www.unidata.ucar.edu/software/netcdf/workshops/2011/datamodels/NcCVars.html
But this change causes missing "reference_time" value in merged netcdfs as it only stores the value from the first file;

2) Fix bug in "time_bounds" variable;

3) Add "pyspatialite" as a optional dependency in spatial query. Will try loading pysqlite2 by default, if failed, try loading pyspatialite lib.
Note: Installation of pyspatialite needs several manual steps on linux, but it is so far a good way for CentOS. On Ubuntu and Windows, user should install pysqlite2 + mod_spatialite binary;

1) Add two new flags, one for 2D grid file (forcing/land/terrain) and one for 1D file (channel/reservoir), to specify whether to keep original dimension size unchanged in resulting outputs.

1-1) If True, the sizes of dimension 'x' and 'y' for 2D grid resulting file and 'feature_id' for 1D resulting file will be same as their originals;
Variables outside subsetting domain will be set to corresponding Missing Data Values.

1-2) If False, the size of above dimension will be shrunk to cover subsetting domain.

Note: keep original dimension unchanged will slightly increase output size for both 1D and 2D files and significantly slow down subsetting process for 1D file.

2) Add python dependencies to setup.py file.

Use a new approach to perform spatial query on grid cell indices against forcing, land and terrain files; Further improve spatial query speed on grid cells; Further address partially covered grids caused by projection distortion; Deprecate Tiff supporting files. Now the only necessary supporting file is the sqlite/spatialite geodatabase for stream, reservoir and HUCs; Remove GDAL; Add pyproj and numpy to dependency list;