Upgrade MPAS to version 8.3.1 (#396)

### Tag name (required for release branches):

None

### Originator(s):

kuanchihwang

### Descriptions (include the issue title, and the keyword ['closes',
'fixes', 'resolves'] followed by the issue number):

This PR upgrades MPAS from version 8.2.1 to 8.3.1.

Version 8.3.0 was released during the Joint MPAS/WRF Users Workshop 2025
on June 2. Version 8.3.1 quickly followed on June 17.

The release notes of MPAS can be found at:
[8.2.2](https://github.com/MPAS-Dev/MPAS-Model/releases/tag/v8.2.2),
[8.2.3](https://github.com/MPAS-Dev/MPAS-Model/releases/tag/v8.2.3),
[8.3.0](https://github.com/MPAS-Dev/MPAS-Model/releases/tag/v8.3.0),
[8.3.1](https://github.com/MPAS-Dev/MPAS-Model/releases/tag/v8.3.1).

### Describe any changes made to the build system:

None

### Describe any changes made to the namelist:

None

### List any changes to the defaults for the input datasets (e.g.,
boundary datasets):

None

### List all files eliminated and why:

```
D       src/dynamics/mpas/assets/0001-Prefix-all-MPAS-namelist-group-and-option-names.patch
D       src/dynamics/mpas/assets/0002-Disable-physics-for-MPAS-dycore-only-build.patch
D       src/dynamics/mpas/assets/0003-Declare-constants-at-the-native-precision-of-MPAS.patch
  * Remove old patches that have been upstreamed
```

### List all files added and what they do:

None

### List all existing files that have been modified, and describe the
changes:

```
M       .gitmodules
M       src/dynamics/mpas/dycore
  * Upgrade MPAS to version 8.3.1
M       src/dynamics/mpas/driver/dyn_mpas_subdriver.F90
  * Add a new `version` global attribute to all stream output files
R100    src/dynamics/mpas/assets/ford-config.md src/dynamics/mpas/assets/ford_config.md
  * Use underscore for filename
```

### Regression tests:

No changes to any existing tests. All tests pass with respect to the
last baseline, `sima0_06_000`.

Author: kuanchihwang

.gitmodules

@@ -14,7 +14,7 @@
         path          = src/dynamics/mpas/dycore
         url           = https://github.com/MPAS-Dev/MPAS-Model.git
         fxsparse      = ../.mpas_sparse_checkout
-        fxtag         = v8.2.1
+        fxtag         = v8.3.1
         fxrequired    = AlwaysRequired
         fxDONOTUSEurl = https://github.com/MPAS-Dev/MPAS-Model.git
 [submodule "ncar-physics"]

src/dynamics/mpas/assets/0001-Prefix-all-MPAS-namelist-group-and-option-names.patch

@@ -1645,6 +1645,7 @@ subroutine dyn_mpas_init_stream_with_pool(self, mpas_pool, mpas_stream, pio_file
             call add_stream_attribute('git_version', self % domain_ptr % core % git_version)
             call add_stream_attribute('model_name', self % domain_ptr % core % modelname)
             call add_stream_attribute('source', self % domain_ptr % core % source)
+            call add_stream_attribute('version', self % domain_ptr % core % modelversion)
 
             ! Attributes related to MPAS domain (i.e., `domain_type`).
             call add_stream_attribute('is_periodic', self % domain_ptr % is_periodic)