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diff --git a/docs/100_about_this_doc.md → docs/CONTRIBUTING.md b/docs/100_about_this_doc.md → docs/CONTRIBUTING.md
diff --git a/docs/98_FAQ.md → docs/FAQ.md b/docs/98_FAQ.md → docs/FAQ.md
diff --git a/docs/99_glossary.md → docs/glossary.md b/docs/99_glossary.md → docs/glossary.md
diff --git a/docs/index.md b/docs/index.md
@@ -8,18 +8,18 @@ style="width: 350px; height: auto; display: block; margin-left: auto;  margin-ri
 ## How to use this documentation
 
 - If you want to know more about the ReproSchema project, its goals and the problems
-it tries to solve: check out our [introduction](./01_introduction.md).
+it tries to solve: check out our [introduction](./introduction.md).
 
 - The ReproSchema is related to the `Semantic Web` and relies on `linked data`
 and the `JSON-LD` format. If you are unfamiliar with such things, head over to
-our [FAQ](./98_FAQ.md). You do not need an in depth understanding of what those
+our [FAQ](./FAQ.md). You do not need an in depth understanding of what those
 things are to use the ReproSchema but some "big picture" conceptual understanding
 could save you from a lot of confusion. 😉
 
-- Not sure how the project is organized? Check out the [project structure](./20_project_structure.md)
+- Not sure how the project is organized? Check out the [project structure](./project_structure.md)
 page.
 
-- Want more details on how the `Reproschema` itself is structured: check out our [schema page](./30_schema)
+- Want more details on how the `Reproschema` itself is structured: check out our [schema page](./schema.md)
 
 <!-- - If you want to use the schema to create your own questionnaire: check out our
 
@@ -43,4 +43,4 @@ is unclear by [opening an issue on our repository](https://github.com/ReproNim/r
 You can also get in touch on [our channel on the mattermost Brainhack](https://mattermost.brainhack.org/brainhack/channels/repronim-reproschema).
 
 If you want to get started right away and contribute directly to this
-documentation,you can find references and how-to in the [about section](./100_about_this_doc.md).
+documentation,you can find references and how-to in the [about section](./CONTRIBUTING.md).
diff --git a/docs/01_introduction.md → docs/introduction.md b/docs/01_introduction.md → docs/introduction.md
diff --git a/docs/20_project_structure.md → docs/project_structure.md b/docs/20_project_structure.md → docs/project_structure.md
@@ -33,7 +33,7 @@ The ReproSchema is like a blueprint for research projects, ensuring everyone col
 
 There is also an [`example`](https://github.com/ReproNim/reproschema/tree/master/examples)
 schema that can help give you a quick overview of what the protocol and activity
-for a study might look like. For more details see the [schema section](30_schema.md).
+for a study might look like. For more details see the [schema section](schema.md).
 
 ## [reproschema-library](https://github.com/ReproNim/reproschema-library)
 
@@ -72,7 +72,8 @@ You can see it in action [here](https://www.repronim.org/reproschema-ui/)
 
 ## [reproschema-protocol-cookiecutter](https://github.com/ReproNim/reproschema-protocol-cookiecutter)
 
-The reproschema-protocol-cookiecutter is a straightforward tool that helps you quickly set up a research study. It offers a ready-to-use template for organizing your study's structure and surveys, ensuring everything meets standard guidelines. Think of it as a quick-start guide to get your research project up and running smoothly. A step-by-step guide see [here](41_create_new_protocol.md).
+The reproschema-protocol-cookiecutter is a straightforward tool that helps you quickly set up a research study. It offers a ready-to-use template for organizing your study's structure and surveys, ensuring everything meets standard guidelines. Think of it as a quick-start guide to get your research project up and running smoothly.
+A step-by-step guide see [here](user_guide/create_new_protocol.md).
 
 ## Other repositories
 

diff --git a/docs/30_schema.md → docs/schema.md b/docs/30_schema.md → docs/schema.md
@@ -25,7 +25,7 @@ You can see an example of those in the [examples folder](https://github.com/Repr
 
 There are in fact more levels than this each and each level has its own schema:
 - all of the schemas can be found in the [`terms` folder](https://github.com/ReproNim/reproschema/terms)
-- the Reproschema actually allows for a more complex level nesting than the one described above (e.g you can have an `activity` wihtin an `activity`)
+- the Reproschema actually allows for a more complex level nesting than the one described above (e.g you can have an `activity` within an `activity`)
 - all the properties of each level are described below in the [Properties of ReproSchema objects section](#properties-of-reproschema-objects)
 
 ## Detailed description

diff --git a/...55_collecting_demographics_information.md → ...ls/collecting_demographics_information.md b/...55_collecting_demographics_information.md → ...ls/collecting_demographics_information.md
diff --git a/docs/tutorials/52_create_new_activity.md → docs/tutorials/create_new_activity.md b/docs/tutorials/52_create_new_activity.md → docs/tutorials/create_new_activity.md
diff --git a/docs/tutorials/51_create_new_protocol.md → docs/tutorials/create_new_protocol.md b/docs/tutorials/51_create_new_protocol.md → docs/tutorials/create_new_protocol.md
diff --git a/...rials/53_tips_to_make_your_life_easier.md → ...utorials/tips_to_make_your_life_easier.md b/...rials/53_tips_to_make_your_life_easier.md → ...utorials/tips_to_make_your_life_easier.md
diff --git a/docs/tutorials/54_translating_an_activity.md → docs/tutorials/translating_an_activity.md b/docs/tutorials/54_translating_an_activity.md → docs/tutorials/translating_an_activity.md
diff --git a/docs/tutorials/50_using_reproschema.md → docs/tutorials/using_reproschema.md b/docs/tutorials/50_using_reproschema.md → docs/tutorials/using_reproschema.md
diff --git a/docs/user_guide/42_adopt_assessments.md → docs/user_guide/adopt_assessments.md b/docs/user_guide/42_adopt_assessments.md → docs/user_guide/adopt_assessments.md
diff --git a/docs/user_guide/43_create_new_assess.md → docs/user_guide/create_new_assess.md b/docs/user_guide/43_create_new_assess.md → docs/user_guide/create_new_assess.md
diff --git a/docs/user_guide/41_create_new_protocol.md → docs/user_guide/create_new_protocol.md b/docs/user_guide/41_create_new_protocol.md → docs/user_guide/create_new_protocol.md
diff --git a/docs/user_guide/45_finalize_protocol.md → docs/user_guide/finalize_protocol.md b/docs/user_guide/45_finalize_protocol.md → docs/user_guide/finalize_protocol.md
diff --git a/docs/user_guide/44_setup_feedback.md → docs/user_guide/setup_feedback.md b/docs/user_guide/44_setup_feedback.md → docs/user_guide/setup_feedback.md
diff --git a/docs/user_guide/46_tools.md → docs/user_guide/tools.md b/docs/user_guide/46_tools.md → docs/user_guide/tools.md
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -16,33 +16,33 @@ theme:
 # Pages
 nav:
   - Welcome: "index.md"
-  - Introduction: "01_introduction.md"
-  - Project structure: "20_project_structure.md"
-  - Schema: "30_schema.md"
+  - Introduction: "introduction.md"
+  - Project structure: "project_structure.md"
+  - Schema: "schema.md"
   - User Guide:
-      - Create a research protocol: "41_create_new_protocol.md"
-      - Adopt assessments from the library: "42_adopt_assessments.md"
-      - Create new assessments for a protocol: "43_create_new_assess.md"
-      - Add a feedback section: "44_setup_feedback.md"
-      - Finalize the protocol: "45_finalize_protocol.md"
-      - Toolkit: "46_tools.md"
+      - Create a research protocol: "user_guide/create_new_protocol.md"
+      - Adopt assessments from the library: "user_guide/adopt_assessments.md"
+      - Create new assessments for a protocol: "user_guide/create_new_assess.md"
+      - Add a feedback section: "user_guide/setup_feedback.md"
+      - Finalize the protocol: "user_guide/finalize_protocol.md"
+      - Toolkit: "user_guide/tools.md"
   - Tutorial:
-      - Intro: "50_using_reproschema.md"
-      - Create a research protocol: "51_create_new_protocol.md" 
-      - Creating a new activity: "52_create_new_activity.md"
-      - Tips to make your life easier: "53_tips_to_make_your_life_easier.md"
-      - Translate a questionnaire: "54_translating_an_activity.md"
-      - Demographic information : "55_collecting_demographics_information.md"
+      - Intro: "tutorials/using_reproschema.md"
+      - Create a research protocol: "tutorials/create_new_protocol.md"
+      - Creating a new activity: "tutorials/create_new_activity.md"
+      - Tips to make your life easier: "tutorials/tips_to_make_your_life_easier.md"
+      - Translate a questionnaire: "tutorials/translating_an_activity.md"
+      - Demographic information : "tutorials/collecting_demographics_information.md"
   # - Creating a new activity and protocol: "create_new_activity_protocol.md"
   # - Testing your schema and collecting data: "testing_using_schema.md"
   # - Contribute to the project:
   #     - ReproSchema: "81_contribute_to_schema.md"
   #     - Assesement library: "82_contribute_to_library.md"
   #     - Python package: "83_contribute_to_python.md"
   #     - User-interface: "84_contribute_to_ui.md"
-  - FAQ: "98_FAQ.md"
-  - Glossary: "99_glossary.md"
-  - About this doc: "100_about_this_doc.md"
+  - FAQ: "FAQ.md"
+  - Glossary: "glossary.md"
+  - Contributing: "CONTRIBUTING.md"
 
 # list of extension
 markdown_extensions:
@@ -55,4 +55,4 @@ markdown_extensions:
       pygments_lang_class: true
   - pymdownx.inlinehilite
   - pymdownx.snippets
-  - pymdownx.superfences
+  - pymdownx.superfences