diff --git a/ndi_common/.matlab2markdown-ignore b/ndi_common/.matlab2markdown-ignore
deleted file mode 100644
index e69de29bb..000000000
diff --git a/src/ndi/docs/NDI-matlab/manual/Document_Design.md b/src/ndi/docs/NDI-matlab/manual/developer/Document_Design.md
similarity index 100%
rename from src/ndi/docs/NDI-matlab/manual/Document_Design.md
rename to src/ndi/docs/NDI-matlab/manual/developer/Document_Design.md
diff --git a/src/ndi/docs/NDI-matlab/manual/NDI_Calculator_Manual.md b/src/ndi/docs/NDI-matlab/manual/developer/NDI_Calculator_Manual.md
similarity index 100%
rename from src/ndi/docs/NDI-matlab/manual/NDI_Calculator_Manual.md
rename to src/ndi/docs/NDI-matlab/manual/developer/NDI_Calculator_Manual.md
diff --git a/src/ndi/docs/manual/developer/cloud.md b/src/ndi/docs/NDI-matlab/manual/developer/cloud.md
similarity index 100%
rename from src/ndi/docs/manual/developer/cloud.md
rename to src/ndi/docs/NDI-matlab/manual/developer/cloud.md
diff --git a/src/ndi/docs/NDI-matlab/manuals/documentTips.md b/src/ndi/docs/NDI-matlab/manual/developer/documentTips.md
similarity index 100%
rename from src/ndi/docs/NDI-matlab/manuals/documentTips.md
rename to src/ndi/docs/NDI-matlab/manual/developer/documentTips.md
diff --git a/src/ndi/docs/NDI-matlab/manuals/implementingNDIQueries.md b/src/ndi/docs/NDI-matlab/manual/developer/implementingNDIQueries.md
similarity index 100%
rename from src/ndi/docs/NDI-matlab/manuals/implementingNDIQueries.md
rename to src/ndi/docs/NDI-matlab/manual/developer/implementingNDIQueries.md
diff --git a/src/ndi/docs/NDI-matlab/mkdocs-start.yml b/src/ndi/docs/NDI-matlab/mkdocs-start.yml
index 18eb7da87..5473591fd 100644
--- a/src/ndi/docs/NDI-matlab/mkdocs-start.yml
+++ b/src/ndi/docs/NDI-matlab/mkdocs-start.yml
@@ -43,9 +43,6 @@ nav:
         - 3.1 Newbie version of your first electrophysiology experiment with NDI: 'NDI-matlab/tutorials/analyzing_first_physiology_experiment_detailed/1_example_dataset.md'
       - 4 Datasets:
         - Francesconi_et_al_2025: 'NDI-matlab/tutorials/datasets/Francesconi_et_al_2025/1_getting_started.md'
-      - 5 Manual:
-        - Developer Manual:
-          - Cloud: 'manual/developer/cloud.md'
       - 7 Writing your own apps and calculators:
         - 7.2 Writing short calculations: 'NDI-matlab/tutorials/writing_own_app/2_ndi_calculators.md'
       - Planned:
@@ -54,4 +51,11 @@ nav:
         - 6. Making your own analysis app that uses NDI: 'NDI-matlab/tutorials/analysis_app.md'
         - 7. Submitting your data to an archive: 'NDI-matlab/tutorials/archive.md'
         - 8. Search and analyze NDI databases on the web: 'NDI-matlab/tutorials/search_ndi_databases.md'
+    - Manual (in progress):
+       - User manual:
+         - Queries: 'NDI-matlab/manual/Queries.md'
+       - Developer Manual:
+         - Cloud: 'NDI-matlab/manual/developer/cloud.md'
+         - Calculators: 'NDI-matlab/manual/developer/NDI_Calculator_Manual.md'
+         - Documents: 'NDI-matlab/manual/developer/Document_Design.md'
     - Document reference: