treeppl · vresbok · Dec 12, 2025
diff --git a/docs/Python-environment/index.md b/docs/Python-environment/index.md
diff --git a/docs/language-reference/distributions.md → docs/distributions.md b/docs/language-reference/distributions.md → docs/distributions.md
@@ -1,3 +1,8 @@
+---
+id: distriutions
+sidebar_position: 8
+---
+
 # Distributions
 
 ## Available distributions

diff --git a/docs/examples/index.md b/docs/examples/index.md
@@ -1,6 +1,6 @@
 ---
 id: models
-sidebar_position: 3
+sidebar_position: 10
 ---
 
 # Model examples

diff --git a/docs/examples/metabarcoding.md b/docs/examples/metabarcoding.md
@@ -2,6 +2,7 @@
 id: metabarcoding
 title: Abundances from metabarcoding
 sidebar_label: Abundances from metabarcoding
+sidebar_position: 1
 ---
 
 # Abundances from metabarcoding

diff --git a/docs/for-developers/index.md b/docs/for-developers/index.md
@@ -1,6 +1,6 @@
 ---
 id: dev
-sidebar_position: 7
+sidebar_position: 13
 ---
 
 # Contribute to TreePPL development

diff --git a/getting-started/getting-started.md → docs/getting-started.md b/getting-started/getting-started.md → docs/getting-started.md
@@ -1,5 +1,6 @@
 ---
 id: getting-started
+sidebar_position: 2
 ---
 import Tabs from '@theme/Tabs';
 import TabItem from '@theme/TabItem';

diff --git a/getting-started/how_to_cite.md → docs/how_to_cite.md b/getting-started/how_to_cite.md → docs/how_to_cite.md
@@ -1,3 +1,8 @@
+---
+id: how_to_cite
+sidebar_position: 13
+---
+
 # How to cite TreePPL
 
 Please cite the [TreePPL Release Note](https://www.biorxiv.org/content/10.1101/2023.10.10.561673v2) when using TreePPL.

diff --git a/docs/index.md b/docs/index.md
@@ -5,13 +5,19 @@ sidebar_position: 1
 
 # TreePPL Documentation
 
+If you are new to TreePPL, we recommend beginning looking at our [Getting started pages](docs/getting-started).
+
 The TreePPL documentation consists of:
 
- - [Python environment](docs/python-environment), linking to the Python Environment documentation,
-  - [R environment](docs/R-environment), linking to the R Environment documentation,
- - [Model examples](docs/examples), which illustrate key models available in TreePPL,
- - [Language reference](docs/language-reference), which contains a language overview, distributions, inference methods, etc.
+ - [Getting started](docs/getting-started), with instructions for first steps,
+ - [Python interface](docs/python-interface), with Python Environment documentation,
+ - [Jupyter interface](docs/jupyter-interface), with Jupyter documentation,
+ - [R environment](docs/R-environment), linking to the R Environment documentation,
  - [Tutorials](docs/tutorials), in which the user learns by doing something meaningful, towards some achievable goal,
-<!-- - To be added: System, which is documentation for the people who would like to develop the TreePPL language itself -->
+ - [Language overview](docs/language-overview), which contains a basic language description,
+ - [Distributions](docs/distributions), describing available distributions and related information,
+ - [Inference methods](docs/inference), describing available inference techniques,
+ - [Model examples](docs/examples), which illustrate key models available in TreePPL,
+ - [Contribute to TreePPL development](docs/for-developers), which is documentation for the people who would like to develop the TreePPL language itself, including how to install for command-line use.
+ - [How to cite](docs/how_to_cite), with background references.
 
-If you are new to TreePPL, we recommend beginning looking at our [Getting started pages](getting-started/getting-started).
diff --git a/docs/language-reference/inference.md → docs/inference.md b/docs/language-reference/inference.md → docs/inference.md
@@ -1,3 +1,8 @@
+---
+id: inference
+sidebar_position: 9
+---
+
 # Inference methods
 
 TreePPL supports several inference methods.

diff --git a/getting-started/jupyter-interface.md → docs/jupyter-interface.md b/getting-started/jupyter-interface.md → docs/jupyter-interface.md
@@ -1,5 +1,6 @@
 ---
 title: Jupyter interface
+sidebar_position: 4
 ---
 # Jupyter interface
 

diff --git a/docs/language-reference/language-overview.md → docs/language-overview.md b/docs/language-reference/language-overview.md → docs/language-overview.md
@@ -1,3 +1,8 @@
+---
+id: language_overview
+sidebar_position: 7
+---
+
 # Language overview
 
 ## Basic features

diff --git a/docs/language-reference/index.md b/docs/language-reference/index.md
diff --git a/...ng-started/media/treeppl-in-jupyter-1.png → docs/media/treeppl-in-jupyter-1.png b/...ng-started/media/treeppl-in-jupyter-1.png → docs/media/treeppl-in-jupyter-1.png
diff --git a/...ng-started/media/treeppl-in-jupyter-2.png → docs/media/treeppl-in-jupyter-2.png b/...ng-started/media/treeppl-in-jupyter-2.png → docs/media/treeppl-in-jupyter-2.png
diff --git a/...ng-started/media/treeppl-in-jupyter-3.png → docs/media/treeppl-in-jupyter-3.png b/...ng-started/media/treeppl-in-jupyter-3.png → docs/media/treeppl-in-jupyter-3.png
diff --git a/getting-started/python-interface.md → docs/python-interface.md b/getting-started/python-interface.md → docs/python-interface.md
@@ -1,6 +1,7 @@
 ---
 layout: default
 title: Python interface
+sidebar_position: 3
 ---
 # Python interface
 

diff --git a/docs/tutorials/index.md b/docs/tutorials/index.md
@@ -1,6 +1,6 @@
 ---
 id: tutorials
-sidebar_position: 4
+sidebar_position: 6
 ---
 
 # Tutorials

diff --git a/docusaurus.config.js b/docusaurus.config.js
@@ -36,18 +36,6 @@ const config = {
       },
     ],
   ],
-  plugins: [
-    [
-      '@docusaurus/plugin-content-docs',
-      {
-        id: 'getting-started',
-        path: 'getting-started',
-        routeBasePath: 'getting-started',
-        sidebarPath: require.resolve('./sidebarsGettingStarted.js'),
-        // ... other options
-      },
-    ],
-  ],
   themeConfig: {
       docs: {
         sidebar: {
@@ -63,10 +51,10 @@ const config = {
         // },
         items: [
           {
-            to: '/getting-started/getting-started',
+            to: '/docs/getting-started',
             position: 'left',
             label: 'Getting Started',
-            activeBaseRegex: `/getting-started/`
+            activeBaseRegex: '/docs/'
           },
           {
             type: 'doc',