diff --git a/docs/documentation/additional-software.md b/docs/documentation/additional_software.md
similarity index 100%
rename from docs/documentation/additional-software.md
rename to docs/documentation/additional_software.md
diff --git a/docs/documentation/aircraft-design.md b/docs/documentation/aircraft-design.md
deleted file mode 100644
index bb2e5ad25230202a84d405679eb14cf1895530fa..0000000000000000000000000000000000000000
--- a/docs/documentation/aircraft-design.md
+++ /dev/null
@@ -1,13 +0,0 @@
-# Sizing and analysizing!
-Yoho $M = \frac{2}{5}$
-
-!!! tip
-
-
-!!! danger
-
-
-```mermaid
-  graph LR;
-  A-->B
-```
diff --git a/docs/documentation/analysis.md b/docs/documentation/analysis.md
index 3f9b1e9d47005c67b6d1cba550b542319d5ce9a9..e8e36639cddda22ef6240aad0cc4be9593eb3d67 100644
--- a/docs/documentation/analysis.md
+++ b/docs/documentation/analysis.md
@@ -22,7 +22,7 @@ lift mach numbers.
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](aerodynamic_analysis/index.html)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](aerodynamic_analysis/content/index.md)|
 
 ---
 
@@ -39,7 +39,7 @@ For the user, possible changes in the module run configuration can be made in th
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](mission_analysis/index.html)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](mission_analysis/content/index.md)|
 
 ---
 
@@ -50,7 +50,7 @@ The `weight_and_balance_analysis` module calculates sub-masses and total masses
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](weight_and_balance_analysis/index.html)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](weight_and_balance_analysis/content/index.md)|
 
 ---
 
@@ -67,7 +67,7 @@ The parameters comprised in this XML file can have different attributes as e.g.
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](ecological_assessment/index.html)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](ecological_assessment/content/index.md)|
 
 ---
 
@@ -78,7 +78,7 @@ The module `calculatePerformance` is used to evaluate the mission performance of
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus:| GPLv3 |[Link](performance_assessment/index.html)|
+|2.1.0|:simple-cplusplus:| GPLv3 |[Link](performance_assessment/content/index.md)|
 
 ---
 
@@ -94,6 +94,6 @@ Direct costs include all expenses incurred in operating and financing the aircra
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-python: |GPLv3|[Link](cost_estimation/index.html)|
+|2.1.0|:simple-python: |GPLv3|[Link](cost_estimation/content/index.md)|
 
 ---
diff --git a/docs/documentation/libraries.md b/docs/documentation/libraries.md
index 7d02739dccabf9182d04be6217eba663cfcd8060..2be0912d110a8f61d1c55a1d478b3c8a85939d88 100644
--- a/docs/documentation/libraries.md
+++ b/docs/documentation/libraries.md
@@ -27,7 +27,7 @@ It has helper functions to extract and interpolate data of provided airfoil pola
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link]()|-|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/aerodynamics/content/index.md)|-|
 
 ---
 
@@ -39,7 +39,7 @@ The modularity and flexibility is achieved by using the high performance [Comput
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](aircraftGeometry2/index.html)| [Eigen3](https://eigen.tuxfamily.org/index.php?title=Main_Page), [CGAL](https://www.cgal.org/)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/aircraftGeometry2/content/index.md)| [Eigen3](https://eigen.tuxfamily.org/index.php?title=Main_Page), [CGAL](https://www.cgal.org/)|
 
 ---
 
@@ -50,7 +50,7 @@ The **airfoils** libary provides a database for different airfoils.
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|1.0.0|:simple-cplusplus: |GPLv3|[Link]()|-|
+|1.0.0|:simple-cplusplus: |GPLv3|[Link](libraries/airfoils/content/index.md)|-|
 
 ---
 
@@ -62,7 +62,7 @@ It uses a simple XML library, namely *tinyxml*, to read and parse the XML files.
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link]()|-|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/aixml/content/index.md)|-|
 
 ---
 
@@ -74,7 +74,7 @@ You can set different atmospheric conditions (e.g. *ISA+25*) and calculate the p
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link]()||
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/atmosphere/content/index.md)||
 
 ---
 
@@ -85,7 +85,7 @@ The **blackboxTest** library provides an interface to run a complete module with
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link]()|[googleTest](https://google.github.io/googletest/)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/blackboxTest/content/index.md)|[googleTest](https://google.github.io/googletest/)|
 
 ---
 
@@ -98,7 +98,7 @@ The engine decks can originate from different softwaretools as long as they prov
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](engine/index.html)|-|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/engine/content/index.md)|-|
 
 ---
 
@@ -118,7 +118,7 @@ It has helper functions to extract and interpolate data of the results from the
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link]()|-|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/liftingLineInterface/content/index.md)|-|
 
 ---
 
@@ -131,7 +131,7 @@ The library gives a template how modules should be structured and gives helpers
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link]()|-|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/moduleBasics/content/index.md)|-|
 
 ---
 
@@ -142,7 +142,7 @@ This library provides standardized UNICADO data preprocessing, run, and postproc
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|1.0.0|:simple-python: |GPLv3|[Link]()|-|
+|1.0.0|:simple-python: |GPLv3|[Link](libraries/pymodulepackage/content/index.md)|-|
 
 ---
 
@@ -154,7 +154,7 @@ In provides custom output streams, which automatically handle the log files and
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link]()|-|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/runtimeInfo/content/index.md)|-|
 
 ---
 
@@ -167,7 +167,7 @@ The library can handle *UNIX* and *Windows* systems alike.
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link]()|-|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/standardFiles/content/index.md)|-|
 
 !!! warning
     Some functions of this library are a bit outdated! When using this library, please look first at the wonderful [STL :octicons-link-external-16:](https://en.cppreference.com/w/) whether the function you are seeking is already there.
@@ -196,4 +196,4 @@ In addition, it defines some common **constants** which are useful for calculati
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link]()|-|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/unitConversion/content/index.md)|-|
diff --git a/docs/documentation/sizing.md b/docs/documentation/sizing.md
index c8fe9a4c9b4ec0454b1ce1020f7e4438f80c7cf3..3208f2b41bec2931f2d498b7a61c44f886063390 100644
--- a/docs/documentation/sizing.md
+++ b/docs/documentation/sizing.md
@@ -23,7 +23,7 @@ Furthermore an initial estimation of the takeoff mass is done.
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](initial_sizing/index.html)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](initial_sizing/content/index.md)|
 
 ---
 
@@ -37,7 +37,7 @@ The parameters comprised in this file can have different attributes as e.g. Desc
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](create_mission_xml/index.html)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](create_mission_xml/content/index.md)|
 
 ---
 
@@ -48,7 +48,7 @@ The **fuselage_design** module calculates characteristic parameters and generate
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](fuselage_design/index.html)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](fuselage_design/content/index.md)|
 
 ---
 
@@ -59,7 +59,7 @@ The **wing_design** module calculates characteristic parameter of the aircraft m
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](wing_design/index.html)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](wing_design/content/index.md)|
 
 ---
 
@@ -71,7 +71,7 @@ It takes takes the controllability as wells as the static margin of the aircraft
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](empennage_design/index.html)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](empennage_design/content/index.md)|
 
 ---
 
@@ -82,7 +82,7 @@ It takes takes the controllability as wells as the static margin of the aircraft
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-python: |GPLv3|[Link](tank_design/index.html)|
+|2.1.0|:simple-python: |GPLv3|[Link](tank_design/content/index.md)|
 
 
 ---
@@ -111,7 +111,7 @@ The **landing_gear_design** module calculates characteristic parameters for the
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](landing_gear_design/index.html)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](landing_gear_design/content/index.md)|
 
 ---
 
@@ -123,6 +123,6 @@ It dimensions ATA chapter systems in terms of mass and energy requirement divide
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](systems_design/index.html)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](systems_design/content/index.md)|
 
 ---
diff --git a/mkdocs.yml b/mkdocs.yml
index 40120f1c7fbdf025bc50d3e8efbc304a6490e374..d662897c386c4967621d023eecda00122c225738 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -68,15 +68,15 @@ plugins:
         propulsion_design:
           src-dirs: ../aircraft-design/propulsion_design/
           full-doc: True
-          output: docs/propulsion_design
           doxy-cfg:
-            FILE_PATTERNS: "*.cpp *.h"
+            FILE_PATTERNS: "*.cpp *.h *.md *.png *.svg" # Include .cpp, .h, .md, .png, .svg files in the documentation
             RECURSIVE: True
             EXTRACT_ALL: YES
+            OUTPUT_DIRECTORY: docs/propulsion_design
         initial_sizing:
           src-dirs: ../aircraft-design/initial_sizing/
           full-doc: true
-          output: docs/initial_sizing
+          output: docs/documentation/initial_sizing/
           doxy-cfg:
             FILE_PATTERNS: "*.cpp *.h"
             RECURSIVE: True
@@ -134,37 +134,51 @@ nav:                                      # Customizes the main navigation struc
   - Documentation:                        # Top-level item for documentation.
       - Overview: 'documentation/overview.md'   # Overview of modules.
       - Aircraft Design:
-          - Introduction: documentation/aircraft-design.md                   # Subsection for Aircraft Design.
+          - Introduction: documentation/aircraft_design.md                   # Subsection for Aircraft Design.
           - Sizing:
-            - Modules: documentation/sizing.md
+            - Sizing Tools: documentation/sizing.md
             - Initial Sizing:
-              - Introduction: 'documentation/initial_sizing/content/index.md'
-              - Getting Started: 'documentation/initial_sizing/content/getting-started.md'
+              - Introduction: 'documentation/initial_sizing/index.md'
+              - Getting Started: 'documentation/initial_sizing/getting-started.md'
               - API Reference: 
-                - initial_sizing/classed.md
-                - initial_sizing/namespaces.md
-                - initial_sizing/files.md
-                - initial_sizing/pages.md
+                - documentation/initial_sizing/classed.md
+                - documentation/initial_sizing/namespaces.md
+                - documentation/initial_sizing/files.md
+                - documentation/initial_sizing/pages.md
             - Propulsion Design:
-              - Introduction: 'documentation/propulsion_design/content/index.md'
-              - Engineering Principles: 'documentation/propulsion_design/content/engineering_principles.md'
-              - Getting Started: 'documentation/propulsion_design/content/getting_started.md'
-              - Software Architecture: 'documentation/propulsion_design/content/software_architecture.md'
+              - Introduction: 'documentation/propulsion_design/index.md'
+              - Engineering Principles: 'documentation/propulsion_design/engineering_principles.md'
+              - Getting Started: 'documentation/propulsion_design/getting_started.md'
+              - Software Architecture: 'documentation/propulsion_design/software_architecture.md'
               - Tutorial:
-                - Main: 'documentation/propulsion_design/content/tutorial.md'
-                - Engine Extension: 'documentation/propulsion_design/content/tutorial_engine_extension.md'
-                - Fidelity Extension: 'documentation/propulsion_design/content/tutorial_fidelity_extension.md'
-              - Additional: 'documentation/propulsion_design/content/additional.md'
+                - Main: 'documentation/propulsion_design/tutorial.md'
+                - Engine Extension: 'documentation/propulsion_design/tutorial_engine_extension.md'
+                - Fidelity Extension: 'documentation/propulsion_design/tutorial_fidelity_extension.md'
+              - Additional: 'documentation/propulsion_design/additional.md'
               - API Reference:
-                - propulsion_design/classes.md
-                - propulsion_design/namespaces.md
-                - propulsion_design/files.md
-                - propulsion_design/pages.md
+                - documentation/propulsion_design/classes.md
+                - documentation/propulsion_design/namespaces.md
+                - documentation/propulsion_design/files.md
+                - documentation/propulsion_design/pages.md
           - Analsysis:
-            - Modules: 'documentation/analysis.md'         # Link to analysis module page.
-      - Libraries: 'documentation/libraries.md' # Link to libraries overview.
-      - Utilities: 'documentation/additional-software.md'  # Link to additional software page.
-      - Workflow: 'workflow.md'           # Link to the workflow page.
+            - Analysis Tools: 'documentation/analysis.md'# Link to analysis module page.
+            - Aerodynamic analysis: 'documentation/aerodynamic_analysis/aerodynamic_analysis.md'
+            - Mission analysis: 'documentation/mission_analysis/mission_analysis.md'
+            - Weight and balance analysis: 'documentation/weight_and_balance_analysis/weight_and_balance_analysis.md'
+            - Ecological assessment: 'documentation/ecological_assessment/ecological_assessment.md'
+            - Performance assessment: 'documentation/performance_assessment/performance_assessment.md'
+            - Cost estimation: 'documentation/cost_estimation/cost_estimation.md'
+      - Libraries: 
+        - Introduction: 'documentation/libraries.md' # Link to libraries overview.
+        - aircraftGeometry2: 'documentation/libraries/aircraftGeometry2/index.md'
+        - airfoils: 'documentation/libraries/airfoils/index.md'
+      - Utilities:
+        - Additional Software: documentation/additional_software.md
+        - cpacs Interface: 'documentation/additional_software/cpacsInterface.md'
+        - designEvaluator: 'documentation/additional_software/cpacsInterface.md'
+        - reportGenerator: 'documentation/additional_software/cpacsInterface.md'
+        - testFramework: 'documentation/additional_software/cpacsInterface.md'
+      - Workflow: 'workflow.md' # Link to the workflow page.
   - Get involved:
       - Developer Guide: developer/developer-installation.md # Top-level item for contributions and development.
       - Build Instructions: