diff --git a/.github/workflows/apply-howto-branches.yml b/.github/workflows/apply-howto-branches.yml
deleted file mode 100644
index d01757887c..0000000000
--- a/.github/workflows/apply-howto-branches.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-name: Apply HOWTO diffs to branches
-on: 
-  push:
-    branches:
-      - master
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@master
-      with:
-        ref: master
-    - name: Apply diffs to branches
-      run: ./howtos/scripts/apply_howto_diffs.sh
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 6c01b62119..9617e07aa6 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -37,9 +37,6 @@ jobs:
     - name: Test with pytest and generate coverage report
       run: |
         tests/run_all_tests.sh --with-cov
-    - name: Check HOWTO patches
-      run: |
-        howtos/scripts/check_howto_diffs.sh
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1
       with:
diff --git a/docs/examples.rst b/docs/examples.rst
index 5f76f53509..bc9eb4351d 100644
--- a/docs/examples.rst
+++ b/docs/examples.rst
@@ -7,8 +7,8 @@ Core examples
 Each example is designed to be self-contained and easily forkable, while
 reproducing relevant results in different areas of machine learning. These
 examples adhere to a shared style and functionality outlined in `#231`_. All
-examples are under the folder `flax/linen_examples/
-<https://github.com/google/flax/tree/master/linen_examples/>`__. Some of the
+examples are under the folder `flax/examples/
+<https://github.com/google/flax/tree/master/examples/>`__. Some of the
 examples below have a link [Interactive] that lets you run them directly in
 Colab.
 
@@ -17,35 +17,35 @@ Colab.
 
 Image classification
 
-   -  `MNIST <https://github.com/google/flax/tree/master/linen_examples/mnist/>`__ [`Interactive
-      <https://colab.research.google.com/github/google/flax/blob/master/linen_examples/mnist/mnist.ipynb>`__] :
+   -  `MNIST <https://github.com/google/flax/tree/master/examples/mnist/>`__ [`Interactive
+      <https://colab.research.google.com/github/google/flax/blob/master/examples/mnist/mnist.ipynb>`__] :
       Convolutional neural network for MNIST classification (featuring simple code).
-   -  `ImageNet <https://github.com/google/flax/tree/master/linen_examples/imagenet/>`__ :
+   -  `ImageNet <https://github.com/google/flax/tree/master/examples/imagenet/>`__ :
       Resnet-50 on imagenet with weight decay (featuring multi host SPMD, custom
       preprocessing, checkpointing, dynamic scaling, mixed precision).
 
 Reinforcement Learning
 
    -  `Proximal Policy
-      Optimization <https://github.com/google/flax/tree/master/linen_examples/ppo/>`__ :
+      Optimization <https://github.com/google/flax/tree/master/examples/ppo/>`__ :
       Learning to play Atari games (featuring single host SPMD, RL setup).
 
 Natural language processing
 
    -  `Sequence to sequence for number
-      addition <https://github.com/google/flax/tree/master/linen_examples/seq2seq/>`__
+      addition <https://github.com/google/flax/tree/master/examples/seq2seq/>`__
       (featuring simple code, LSTM state handling, on the fly data generation).
    -  `Transformer model on
-      WMT <https://github.com/google/flax/tree/master/linen_examples/wmt/>`__ :
+      WMT <https://github.com/google/flax/tree/master/examples/wmt/>`__ :
       Translating English/German (featuring multihost SPMD, dynamic bucketing, attention cache,
       packed sequences, recipe for TPU training on GCP).
 
 Generative models
 
    -  `Variational
-      auto-encoder <https://github.com/google/flax/tree/master/linen_examples/vae/>`__ :
+      auto-encoder <https://github.com/google/flax/tree/master/examples/vae/>`__ :
       Trained on binarized MNIST (featuring simple code, vmap).
-   -  `PixelCNN++ <https://github.com/google/flax/tree/master/linen_examples/pixelcnn/>`__ :
+   -  `PixelCNN++ <https://github.com/google/flax/tree/master/examples/pixelcnn/>`__ :
       Trained on cifar10 (featuring single host SPMD, checkpointing, Polyak decay).
 
 
diff --git a/docs/notebooks/linen_intro.ipynb b/docs/notebooks/linen_intro.ipynb
index 9ef1d47c2a..c08b9fc1e7 100644
--- a/docs/notebooks/linen_intro.ipynb
+++ b/docs/notebooks/linen_intro.ipynb
@@ -38,9 +38,9 @@
         "\n",
         "⟶ [Slides](https://docs.google.com/presentation/d/1ngKWUwsSqAwPRvATG8sAxMzu9ujv4N__cKsUofdNno0/edit?usp=sharing) for the core ideas of the new Functional Core and Linen\n",
         "\n",
-        "⟶ \"Design tests\" guided our design process. Many are available for [functional core](https://github.com/google/flax/tree/linen2/linen_examples/core_design_test) and some for the [proposed Module abstraction](https://github.com/google/flax/tree/linen2/linen_examples/linen_design_test/)\n",
+        "⟶ \"Design tests\" guided our design process. Many are available for [functional core](https://github.com/google/flax/tree/master/examples/core_design_test) and some for the [proposed Module abstraction](https://github.com/google/flax/tree/master/examples/linen_design_test/)\n",
         "\n",
-        "⟶ Ported examples: [ImageNet](https://github.com/google/flax/tree/linen2/linen_examples/imagenet) and [WMT](https://github.com/google/flax/tree/linen2/linen_examples/wmt) (to the proposed Module abstraction). TODO: Port to functional core.\n",
+        "⟶ Ported examples: [ImageNet](https://github.com/google/flax/tree/master/examples/imagenet) and [WMT](https://github.com/google/flax/tree/master/examples/wmt) (to the proposed Module abstraction). TODO: Port to functional core.\n",
         "\n",
         "⟶ Our new [discussion forums](https://github.com/google/flax/discussions/)\n",
         "\n"
diff --git a/flax/linen_examples/README.md b/linen_examples/README.md
similarity index 100%
rename from flax/linen_examples/README.md
rename to linen_examples/README.md
diff --git a/linen_examples/vae/results/.gitignore b/linen_examples/vae/results/.gitignore
deleted file mode 100644
index aab52d906f..0000000000
--- a/linen_examples/vae/results/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-*.png
\ No newline at end of file