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diff --git a/.github/ISSUE_TEMPLATE/README.md b/.github/ISSUE_TEMPLATE/README.md
@@ -0,0 +1,10 @@
+## 'ISSUE_TEMPLATE' Directory Contents
+
+### Files
+
+bug_report.yml
+
+feature_request.yaml
+
+voxl.yml
+
diff --git a/.github/workflows/README.md b/.github/workflows/README.md
@@ -0,0 +1,6 @@
+## 'workflows' Directory Contents
+
+### Files
+
+main.yml
+
diff --git a/bin/README.md b/bin/README.md
@@ -0,0 +1,6 @@
+## 'PIXL/bin' Directory Contents
+
+### Subdirectories
+
+[linters](./linters/README.md)
+
diff --git a/bin/linters/README.md b/bin/linters/README.md
@@ -0,0 +1,6 @@
+## 'PIXL/bin/linters' Directory Contents
+
+### Files
+
+check_headers_exist.sh
+
diff --git a/cli/README.md b/cli/README.md
@@ -142,3 +142,18 @@ The CLI tests require a running instance of the `rabbitmq` service, for which we
 pytest -vs tests #for all tests
 pytest -vs tests/test_docker_commands.py #e.g., for particular tests
 ```
+
+## 'PIXL/cli' Directory Contents
+
+### Subdirectories
+
+[src](./src/README.md)
+
+[tests](./tests/README.md)
+
+### Files
+
+pyproject.toml
+
+README.md
+
diff --git a/cli/src/README.md b/cli/src/README.md
@@ -0,0 +1,6 @@
+## 'PIXL/cli/src' Directory Contents
+
+### Subdirectories
+
+[pixl_cli](./pixl_cli/README.md)
+
diff --git a/cli/src/pixl_cli/README.md b/cli/src/pixl_cli/README.md
@@ -0,0 +1,18 @@
+## 'PIXL/cli/src/pixl_cli' Directory Contents
+
+### Files
+
+main.py
+
+_config.py
+
+_database.py
+
+_docker_commands.py
+
+_io.py
+
+_message_processing.py
+
+__init__.py
+
diff --git a/cli/tests/README.md b/cli/tests/README.md
@@ -5,3 +5,25 @@ Remove the db container and associated data
 docker container rm pixl-test-db -v -f
 ```
 
+## 'PIXL/cli/tests' Directory Contents
+
+### Files
+
+conftest.py
+
+README.md
+
+test_check_env.py
+
+test_database.py
+
+test_docker_commands.py
+
+test_io.py
+
+test_messages_from_files.py
+
+test_message_processing.py
+
+test_populate.py
+
diff --git a/docker/README.md b/docker/README.md
@@ -0,0 +1,22 @@
+## 'PIXL/docker' Directory Contents
+
+### Subdirectories
+
+[export-api](./export-api/README.md)
+
+[hasher-api](./hasher-api/README.md)
+
+[imaging-api](./imaging-api/README.md)
+
+[orthanc-anon](./orthanc-anon/README.md)
+
+[orthanc-raw](./orthanc-raw/README.md)
+
+[postgres](./postgres/README.md)
+
+### Files
+
+.dockerignore
+
+common.env
+
diff --git a/docker/export-api/README.md b/docker/export-api/README.md
@@ -0,0 +1,6 @@
+## 'PIXL/docker/export-api' Directory Contents
+
+### Files
+
+Dockerfile
+
diff --git a/docker/hasher-api/README.md b/docker/hasher-api/README.md
@@ -0,0 +1,6 @@
+## 'PIXL/docker/hasher-api' Directory Contents
+
+### Files
+
+Dockerfile
+
diff --git a/docker/imaging-api/README.md b/docker/imaging-api/README.md
@@ -0,0 +1,6 @@
+## 'PIXL/docker/imaging-api' Directory Contents
+
+### Files
+
+Dockerfile
+
diff --git a/docker/orthanc-anon/README.md b/docker/orthanc-anon/README.md
@@ -0,0 +1,6 @@
+## 'PIXL/docker/orthanc-anon' Directory Contents
+
+### Files
+
+Dockerfile
+
diff --git a/docker/orthanc-raw/README.md b/docker/orthanc-raw/README.md
@@ -0,0 +1,6 @@
+## 'PIXL/docker/orthanc-raw' Directory Contents
+
+### Files
+
+Dockerfile
+
diff --git a/docker/postgres/README.md b/docker/postgres/README.md
@@ -0,0 +1,6 @@
+## 'PIXL/docker/postgres' Directory Contents
+
+### Files
+
+Dockerfile
+
diff --git a/docs/README.md b/docs/README.md
@@ -0,0 +1,14 @@
+## 'PIXL/docs' Directory Contents
+
+### Subdirectories
+
+[design](./design/README.md)
+
+[file_types](./file_types/README.md)
+
+[joss-publication](./joss-publication/README.md)
+
+[services](./services/README.md)
+
+[setup](./setup/README.md)
+
diff --git a/docs/design/README.md b/docs/design/README.md
@@ -0,0 +1,10 @@
+## 'PIXL/docs/design' Directory Contents
+
+### Subdirectories
+
+[diagrams](./diagrams/README.md)
+
+### Files
+
+bigger_picture.md
+
diff --git a/docs/design/diagrams/README.md b/docs/design/diagrams/README.md
@@ -0,0 +1,8 @@
+## 'PIXL/docs/design/diagrams' Directory Contents
+
+### Files
+
+pixl-multi-project-config.drawio
+
+pixl-multi-project-config.png
+
diff --git a/docs/file_types/README.md b/docs/file_types/README.md
@@ -0,0 +1,6 @@
+## 'PIXL/docs/file_types' Directory Contents
+
+### Files
+
+parquet_files.md
+
diff --git a/docs/joss-publication/README.md b/docs/joss-publication/README.md
@@ -0,0 +1,12 @@
+## 'PIXL/docs/joss-publication' Directory Contents
+
+### Subdirectories
+
+[figures](./figures/README.md)
+
+### Files
+
+paper.bib
+
+paper.md
+
diff --git a/docs/joss-publication/figures/README.md b/docs/joss-publication/figures/README.md
@@ -0,0 +1,2 @@
+## 'PIXL/docs/joss-publication/figures' Directory Contents
+
diff --git a/docs/joss-publication/paper.bib b/docs/joss-publication/paper.bib
diff --git a/docs/joss-publication/paper.md b/docs/joss-publication/paper.md
@@ -0,0 +1 @@
+This is the file where the paper must be written
diff --git a/docs/services/README.md b/docs/services/README.md
@@ -0,0 +1,8 @@
+## 'PIXL/docs/services' Directory Contents
+
+### Files
+
+ftp-server.md
+
+pixl_database.md
+
diff --git a/docs/setup/README.md b/docs/setup/README.md
@@ -0,0 +1,10 @@
+## 'PIXL/docs/setup' Directory Contents
+
+### Files
+
+azure-keyvault.md
+
+developer.md
+
+uclh-infrastructure-setup.md
+
diff --git a/hasher/README.md b/hasher/README.md
@@ -67,3 +67,18 @@ HASHER_API_AZ_CLIENT_PASSWORD=<generated-password>
 HASHER_API_AZ_TENANT_ID=<tenant-ID>
 HASHER_API_AZ_KEY_VAULT_NAME=<key-vault-name>
 ```
+
+## 'PIXL/hasher' Directory Contents
+
+### Subdirectories
+
+[src](./src/README.md)
+
+[tests](./tests/README.md)
+
+### Files
+
+pyproject.toml
+
+README.md
+
diff --git a/hasher/src/README.md b/hasher/src/README.md
@@ -0,0 +1,6 @@
+## 'PIXL/hasher/src' Directory Contents
+
+### Subdirectories
+
+[hasher](./hasher/README.md)
+
diff --git a/hasher/src/hasher/README.md b/hasher/src/hasher/README.md
@@ -0,0 +1,12 @@
+## 'PIXL/hasher/src/hasher' Directory Contents
+
+### Files
+
+endpoints.py
+
+hashing.py
+
+main.py
+
+__init__.py
+
diff --git a/hasher/tests/README.md b/hasher/tests/README.md
@@ -0,0 +1,12 @@
+## 'PIXL/hasher/tests' Directory Contents
+
+### Files
+
+conftest.py
+
+test_endpoints.py
+
+test_hashing.py
+
+__init__.py
+
diff --git a/orthanc/README.md b/orthanc/README.md
@@ -9,3 +9,18 @@ PIXL defines 2 types of ORTHANC instances:
 
 For both instances we define a plugin in `orthanc-*/plugin/pixl.py` that implements the custom
 functionality .
+
+## 'PIXL/orthanc' Directory Contents
+
+### Subdirectories
+
+[assets](./assets/README.md)
+
+[orthanc-anon](./orthanc-anon/README.md)
+
+[orthanc-raw](./orthanc-raw/README.md)
+
+### Files
+
+README.md
+
diff --git a/orthanc/assets/README.md b/orthanc/assets/README.md
@@ -0,0 +1,10 @@
+## 'PIXL/orthanc/assets' Directory Contents
+
+### Files
+
+orthanc-anon-az-dicom.png
+
+orthanc-anon-web.png
+
+orthanc-raw-web.png
+
diff --git a/orthanc/orthanc-anon/README.md b/orthanc/orthanc-anon/README.md
@@ -105,3 +105,18 @@ start.
 ## References
 
 - [Cheat sheet of the REST API](https://book.orthanc-server.com/users/rest-cheatsheet.html)
+
+## 'orthanc' Directory Contents
+
+### Subdirectories
+
+[assets](./assets/README.md)
+
+[orthanc-anon](./orthanc-anon/README.md)
+
+[orthanc-raw](./orthanc-raw/README.md)
+
+### Files
+
+README.md
+
diff --git a/orthanc/orthanc-anon/config/README.md b/orthanc/orthanc-anon/config/README.md
@@ -0,0 +1,8 @@
+## 'PIXL/orthanc/orthanc-anon/config' Directory Contents
+
+### Files
+
+dicom.json
+
+orthanc.json
+
diff --git a/orthanc/orthanc-anon/docs/README.md b/orthanc/orthanc-anon/docs/README.md
@@ -0,0 +1,10 @@
+## 'PIXL/orthanc/orthanc-anon/docs' Directory Contents
+
+### Subdirectories
+
+[assets](./assets/README.md)
+
+### Files
+
+DicomServiceViaAAD.md
+
diff --git a/orthanc/orthanc-anon/docs/assets/README.md b/orthanc/orthanc-anon/docs/assets/README.md
@@ -0,0 +1,6 @@
+## 'PIXL/orthanc/orthanc-anon/docs/assets' Directory Contents
+
+### Files
+
+DicomServiceAuthority.png
+
diff --git a/orthanc/orthanc-anon/plugin/README.md b/orthanc/orthanc-anon/plugin/README.md
@@ -0,0 +1,8 @@
+## 'PIXL/orthanc/orthanc-anon/plugin' Directory Contents
+
+### Files
+
+download_dicom_spec.py
+
+pixl.py
+
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		## 'PIXL/docs/joss-publication/figures' Directory Contents
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		This is the file where the paper must be written