diff --git a/docs/gen_ref_pages.py b/docs/gen_ref_pages.py
index b62a412e1dbe4159e52f3123095ef9cd345f25ff..cf32dc1673108299ffe1cdbaaa87c7975494d226 100644
--- a/docs/gen_ref_pages.py
+++ b/docs/gen_ref_pages.py
@@ -19,9 +19,7 @@ for path in sorted(Path("src").rglob("*.py")):
     if parts[-1] == "__init__":
         parts = parts[:-1]
         print("init parts:", parts)
-    if parts[-1] == "calcat_interface":
-        continue
-    elif parts[-1] == "__main__":
+    if parts[-1] in ["notebooks", "settings", "calcat_interface", "restful_config", "__main__"]:
         continue
 
     nav[parts] = doc_path.as_posix() 
diff --git a/docs/index.md b/docs/index.md
index 888017a1922ae00d504d67d19f0d468e5396ad18..2003c87f9245f8c06f4b82e921ba5960c2269fbe 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -4,18 +4,6 @@ European XFEL Offline Calibration
 The European XFEL Offline Calibration (pyCalibration) is a python package that consists of different services, responsible for applying most of the offline calibration and characterization for the detectors.
 
 
-Documentation contents:
-
 - [Overview](overview.md) Offline calibration overview
 
 - [Installation](development/installation.md) How to install pycalibration
-
-- [Configuration](development/configuration.md) xfel-calibrate CLI configuration
-
-- [Development](development/workflow.md) How to start developing offline calibration notebooks
-
-- [How to write a notebook](how_to_write_xfel_calibrate_notebook_NBC.ipynb) A guide on how to arrange notebook's cells.
-
-- [available_notebooks](available_notebooks.md) The current available production notebooks.
-
-- [calibration_database](calibration_database.md) The calibration database.
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
index 5d0746b985e3741246b6c749159c48a96db91b32..09c6648bd3c98a4992a8997318b81e4f898a9aff 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -101,7 +101,6 @@ nav:
       - Advanced topics: development/advanced.md
     - Code Reference:
       - CALCAT Interface: code_reference/calcat_interface.md
-      - Calibration Tools: code_reference/cal_tools.md
       - Code Reference: reference/
     - Reference:
       - FAQ: references/faq.md