Renaming grid references to mesh.

To use the actual name of the type for the var_struct.
Updating nVertLevels reference in advection.

The CICE core requires the ability to advect using var_arrays that have
a different second dimension. For the purpose, the nVertLevels dimension
is now determined based on the input var_array that should be advected.
Added horizontal interpolation of the 4-layer soil temperature (ST000007,ST007028,
ST028100,and ST100255) and soil moisture (SM000007,SM007028,SM028100,and SM100255)
needed for the initialization of MPAS-A with ERA-interim pressure-level data.
Setup for packages in ocean core.

Defining some packages and attaching variables to packages for use in
the ocean core.
Removing doxygen svn version strings from ocean.

The ocean core previously had SVN keywords in the version line of
doxygen comments.
Always write lowFreqDivergence and highFreqThickness fields, regardless of active package.
Moving the parsing of registry into cores.

This allows cores to do more complicated parsing of registry. Then the
parse executable parses Registry_processed.xml which is the output from
the core target "core_reg".
Reformatting registry source files.

Replacing spaces with tabs.
Adding folds for registry source files
Dividing gen_inc.c up into functions.

Dividing the functions that generate the *.inc files for preprocessing
MPAS source into separate functions.

Each function is intended to write a single file (with the file pointer
passed in). This should allow new developers to more easily determine
how to write a single file similar to another file.
Remove default namelists from repository.

The main repository not longer tracks default namelists.
Auto-generating distinct namelist files.

Registry now is used to generate default namelist files at build time.
Namelist options and records in Registry.xml are allowed to have the
attribute in_defaults which can take the value true or false. By default
this value is false (if it's not specified) meaning the option and/or
record will not be listed in the default generated namelist file. True
will mean registry will include the option/record when writing the
default namelist file.

As a starting place, all namelist records are enabled by default in all
core Registry.xml files. Cores can modify this to disable
options/records they do not want included in the default.

Generated namelist files are named namelist.core_name. Namelist files
for an executable named core_model are also read from namelist.core, so
different executables can read from different namelist files.
Switch Registry parsing code to make use of XML stream definitions for default "iros" streams.
Convert existing Registry.xml files to use XML stream definitions.
Remove code from registry for parsing old stream definitions.

For MPAS cores that are not yet in the MPAS-Dev develop repository,
conversion to the new XML stream definitions can be aided by using code
from the preceding commit: to generate new XML stream definitions, a
core can define the cpp macro OLD_STREAMS in src/registry/parse.c, then
compile the core to have a set of stream definitions printed to standard
output. Adding these definitions to the Registry.xml and removing the
old stream definitions (e.g., ":g/ streams=\"[iros]*\"/s///g") should be
sufficient.
Update XML schema to reflect new stream definition syntax.
Add validation code to ensure that all variables being added to a stream
are actually defined in the Registry file.
Parsing multiple var_structs in registry files.

When the Registry_processed.xml file is being parsed, all
variable structures with the same name are included in the first
instance. So all attributes on variable structures with the same name
use the attributes from the first instance.
Adding additional global attributes

mesh_id - A Unique mesh identifier.
Conventions - Defines the conventions for the file (Presently MPAS, could be CF later).
source - Defines the source for the file (Presently MPAS).
mesh_spec - Defines the mesh specification this file follows.
git_version - Defines the version from a git repository.
Adding removal of *.i to clean targets.

This is for specific versions of intel of specific operating systems.
Some versions create *.i files which are not removed during the clean
process presently.