Fix mkdocs warnings

[paran1]

Fix WARNING/INFO messages when running mkdocs.

• Handle deprecation warnings - change materialx.emoji to material.extensions.emoji
• Fix broken links

With this PR these are no longer logged:

$ mkdocs serve
INFO    -  DeprecationWarning: 'materialx.emoji.twemoji' is deprecated.
           Material emoji logic has been officially moved into mkdocs-material
           version 9.4. Please use Material's 'material.extensions.emoji.twemoji'
           instead of 'materialx.emoji.twemoji' in your 'mkdocs.yml' file.

           ```
           markdown_extensions:
             - pymdownx.emoji:
                 emoji_index: !!python/name:material.extensions.emoji.twemoji
                 emoji_generator: !!python/name:material.extensions.emoji.to_svg
           ```

           'mkdocs_material_extensions' is deprecated and will no longer be
           supported moving forward. This is the last release.

             File "/venv/lib/python3.10/site-packages/materialx/emoji.py", line 118, in twemoji
               return _patch_index(options)
             File "/venv/lib/python3.10/site-packages/materialx/emoji.py", line 68, in _deprecated_func
               warnings.warn(
WARNING -  Material emoji logic has been officially moved into mkdocs-material
           version 9.4. Please use Material's 'material.extensions.emoji.twemoji'
           instead of 'materialx.emoji.twemoji' in your 'mkdocs.yml' file.

           ```
           markdown_extensions:
             - pymdownx.emoji:
                 emoji_index: !!python/name:material.extensions.emoji.twemoji
                 emoji_generator: !!python/name:material.extensions.emoji.to_svg
           ```

           'mkdocs_material_extensions' is deprecated and will no longer be
           supported moving forward. This is the last release.

...

INFO    -  DeprecationWarning: 'materialx.emoji.to_svg' is deprecated.
           Material emoji logic has been officially moved into mkdocs-material
           version 9.4. Please use Material's 'material.extensions.emoji.to_svg'
           instead of 'materialx.emoji.to_svg' in your 'mkdocs.yml' file.

           ```
           markdown_extensions:
             - pymdownx.emoji:
                 emoji_index: !!python/name:material.extensions.emoji.twemoji
                 emoji_generator: !!python/name:material.extensions.emoji.to_svg
           ```

           'mkdocs_material_extensions' is deprecated and will no longer be
           supported moving forward. This is the last release.

             File "/venv/lib/python3.10/site-packages/pymdownx/emoji.py", line 328, in handleMatch
               el = self.generator(
             File "/venv/lib/python3.10/site-packages/materialx/emoji.py", line 68, in _deprecated_func
               warnings.warn(
WARNING -  Material emoji logic has been officially moved into mkdocs-material
           version 9.4. Please use Material's 'material.extensions.emoji.to_svg'
           instead of 'materialx.emoji.to_svg' in your 'mkdocs.yml' file.

           ```
           markdown_extensions:
             - pymdownx.emoji:
                 emoji_index: !!python/name:material.extensions.emoji.twemoji
                 emoji_generator: !!python/name:material.extensions.emoji.to_svg
           ```

           'mkdocs_material_extensions' is deprecated and will no longer be
           supported moving forward. This is the last release.
INFO    -  Doc file 'software/python.md' contains an unrecognized relative link 'Python versions', it was left as is.
INFO    -  Doc file 'software/r.md' contains an unrecognized relative link 'swcarpentry.github.io/r-novice-inflammation/', it was left as is.
INFO    -  Doc file 'cluster_guides/start_interactive_node.md' contains a link '#when-to-use-an-interactive node', but there is no such anchor on this page.
INFO    -  Doc file 'software/beast2.md' contains a link '../getting_started/login_rackham.md#remote-desktop-via-a-ThinLinc client', but the doc
           'getting_started/login_rackham.md' does not contain an anchor '#remote-desktop-via-a-ThinLinc client'.
INFO    -  Doc file 'software/beast2.md' contains a link '../getting_started/login_rackham.md#remote-desktop-via-the-web', but the doc
           'getting_started/login_rackham.md' does not contain an anchor '#remote-desktop-via-the-web'.
INFO    -  Doc file 'software/install.md' contains a link 'compiling_parallel.md#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries', but
           the doc 'software/compiling_parallel.md' does not contain an anchor '#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries'.
INFO    -  Doc file 'software/jobstats.md' contains a link '#jobstats---plot', but there is no such anchor on this page.
INFO    -  Doc file 'software/python_venv.md' contains a link '../software/python.md#loading-python-modules', but the doc 'software/python.md' does not contain an
           anchor '#loading-python-modules'.
INFO    -  Documentation built in 6.60 seconds

[richelbilderbeek]

@paran1 this is great! I've always wanted to fix those warnings too! Will happily merge!