Repository: google/flax

Issue:
We should remove `docs/advanced_topics`
As part of the Flax docs restructuring outlined in #2788, files from *Advanced topics* were moved to different sections in the docs and updated. However the original docs still remain in the [`docs/advanced_topics`](https://github.com/google/flax/tree/main/docs/advanced_topics) folder and can still be viewed on our docs page.

For example, if you search for ["Lifted Transformations"](https://flax.readthedocs.io/en/latest/search.html?q=lifted+transformations) in the search bar, both the original and updated version of the docs show up in the results, which will be confusing for users:
![Screenshot 2023-05-04 at 3 33 36 PM](https://user-images.githubusercontent.com/19753743/236343860-b8822380-623b-4ff6-9bfa-dfae90f744e1.png)

There are also some links that point to the old documentation. The following non-exhaustive list contains some (but not all) examples:
* [`docs/glossary.rst`](https://github.com/google/flax/blob/main/docs/glossary.rst)
* [`linen/recurrent.py`](https://github.com/google/flax/blob/main/flax/linen/recurrent.py#L18)
* [`traverse_util.py`](https://github.com/google/flax/blob/main/flax/traverse_util.py#L201)
* [`docs/getting_started.ipynb`](https://github.com/google/flax/blob/main/docs/getting_started.ipynb)
* [`docs/getting_started.md`](https://github.com/google/flax/blob/main/docs/getting_started.md)

The following is a list of files that were moved from *Advanced topics* in #2788 (this accounts for all files that are in `docs/advanced_topics`):
* How to contribute ([ORIGINAL LOCATION](https://flax.readthedocs.io/en/latest/advanced_topics/contributing.html) --> [NEW LOCATION](https://flax.readthedocs.io/en/latest/contributing.html))
* The Flax philosophy ([ORIGINAL](https://flax.readthedocs.io/en/latest/advanced_topics/philosophy.html) [LOCATIONS](https://flax.readthedocs.io/en/latest/advanced_topics/linen_design_principles.html) --> [NEW LOCATION](https://flax.readthedocs.io/en/latest/philosophy.html))
* Dealing with Module arguments ([ORIGINAL LOCATION](https://flax.readthedocs.io/en/latest/advanced_topics/arguments.html) --> [NEW LOCATION](https://flax.readthedocs.io/en/latest/guides/arguments.html))
* Convert PyTorch models to Flax ([ORIGINAL LOCATION](https://flax.readthedocs.io/en/latest/advanced_topics/convert_pytorch_to_flax.html) --> [NEW LOCATION](https://flax.readthedocs.io/en/latest/guides/convert_pytorch_to_flax.html))
* Upgrade my codebase to Optax ([ORIGINAL LOCATION](https://flax.readthedocs.io/en/latest/advanced_topics/optax_update_guide.html) --> [NEW LOCATION](https://flax.readthedocs.io/en/latest/guides/optax_update_guide.html))
* Upgrade my codebase to Linen ([ORIGINAL LOCATION](https://flax.readthedocs.io/en/latest/advanced_topics/linen_upgrade_guide.html) --> [NEW LOCATION](https://flax.readthedocs.io/en/latest/guides/linen_upgrade_guide.html))
* The Flax Module lifecycle ([ORIGINAL LOCATION](https://flax.readthedocs.io/en/latest/advanced_topics/module_lifecycle.html) --> [NEW LOCATION](https://flax.readthedocs.io/en/latest/developer_notes/module_lifecycle.html))
* Lifted transformations ([ORIGINAL LOCATION](https://flax.readthedocs.io/en/latest/advanced_topics/lift.html) --> [NEW LOCATION](https://flax.readthedocs.io/en/latest/developer_notes/lift.html))
* Flax - The Sharp Bits ([ORIGINAL LOCATION]() --> [NEW LOCATION](https://flax.readthedocs.io/en/latest/notebooks/flax_sharp_bits.html))

Since all original files have been moved and updated, we should remove `docs/advanced_topics` and update all links to point to the new, updated docs.


Discussion:

Resolving patch:
diff --git a/flax/linen/recurrent.py b/flax/linen/recurrent.py
--- a/flax/linen/recurrent.py
+++ b/flax/linen/recurrent.py
@@ -15,7 +15,7 @@
 """Recurrent neural network modules.
 
 THe RNNCell modules can be scanned using lifted transforms. For more information
-see: https://flax.readthedocs.io/en/latest/advanced_topics/lift.html.
+see: https://flax.readthedocs.io/en/latest/developer_notes/lift.html.
 """
 
 from functools import partial   # pylint: disable=g-importing-member
diff --git a/flax/traverse_util.py b/flax/traverse_util.py
--- a/flax/traverse_util.py
+++ b/flax/traverse_util.py
@@ -198,7 +198,7 @@ def __new__(cls, *args, **kwargs):
     warnings.warn(
         '`flax.traverse_util.Traversal` will be deprecated. If you are using '
         'it for `flax.optim`, use `optax` instead. Refer to the update guide '
-        'https://flax.readthedocs.io/en/latest/advanced_topics/optax_update_guide.html '
+        'https://flax.readthedocs.io/en/latest/guides/optax_update_guide.html '
         'for detailed instructions.', DeprecationWarning)
     return super().__new__(cls)
 


Test patch: