diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 01e325d2d5dffa4d4e8a831f5194e18b3d0676d3..18051f02709a781993ad7532fc0a032623cfcd0d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -33,10 +33,10 @@ clone:
       # clone repos
       - git clone https://gitlab-ci-token:${CI_JOB_TOKEN}@git.rwth-aachen.de/unicado/aircraft-design
       - cd aircraft-design
-      - git clone --recurse-submodules https://gitlab-ci-token:${CI_JOB_TOKEN}@git.rwth-aachen.de/unicado/libraries libs/
-    # Change to the project directory (useful for multi-directory repositories)
+      # Clone libraries inside the aircraft-design directory
+      - git clone --recurse-submodules https://gitlab-ci-token:${CI_JOB_TOKEN}@git.rwth-aachen.de/unicado/libraries lib
+      # Change to the project directory (useful for multi-directory repositories)
       - cd $CI_PROJECT_DIR
-      - ls -la $CI_PROJECT_DIR
   artifacts:
     # Save the generated documentation as artifacts so they can be accessed later in the pipeline
     paths:
@@ -49,8 +49,7 @@ clone:
     - if: '$CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH'  # Allow manual triggers on non-default branches
       when: manual  # Run only when triggered manually
     - if: '$CI_PIPELINE_SOURCE == "trigger"'  # Triggered by another pipeline
-      when: on_success  # Run if the source pipeline was successful
-
+      when: on_success  # Run if the source pipeline was successful    
 # === Build and deploy the website ===
 pages:
   image: python:latest
@@ -79,4 +78,6 @@ pages:
     - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH'  # Run when the commit is on the default branch
       when: on_success  # Only run if the previous jobs are successful
     - if: '$CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH'  # Allow manual triggers on non-default branches
-      when: manual  # Run only when triggered manually
\ No newline at end of file
+      when: manual  # Run only when triggered manually
+    - if: '$CI_PIPELINE_SOURCE == "trigger"'  # Triggered by another pipeline
+      when: on_success  # Run if the source pipeline was successful
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
index 6e6613af6d53f685171bb6e3fbd12cae97721371..ccf4f51ab99ea06995e56ccd84a7dfb798901b51 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -73,145 +73,145 @@ plugins:
   - mkdoxy:
       projects:
         propulsion_design:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "propulsion_design"
-            OUTPUT_DIR: "docs/api/propulsion"
-            BIBTEX_FILE: "docs/assets/bibtex/propulsion_design_literature.bib"
-          src-dirs: ../aircraft-design/propulsion_design/src/
-          full-doc: True
-        ecological_assessment:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "ecological_assessment"
-            OUTPUT_DIR: "docs/api/ecological_assessment"
-            BIBTEX_FILE: "docs/assets/bibtex/ecological_assessment_literature.bib"
-          src-dirs: ../aircraft-design/ecological_assessment/src/
+          src-dirs: aircraft-design/propulsion_design/src
           full-doc: True
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+            OUTPUT_DIRECTORY: "./docs/propulsion_design"
+            BIBTEX_FILE: docs/assets/bibtex/propulsion_design_literature.bib
         initial_sizing:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "initial_sizing"
-            OUTPUT_DIR: "docs/api/initial_sizing"
-            BIBTEX_FILE: "docs/assets/bibtex/initial_sizing_literature.bib"
-          src-dirs: ../aircraft-design/initial_sizing/src/
+          src-dirs: aircraft-design/initial_sizing/src
           full-doc: true
+          doxy-cfg:
+            OUTPUT_DIRECTORY: "./docs/initial_sizing"
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
         create_mission_xml:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "create_mission_xml"
-            OUTPUT_DIR: "docs/api/create_mission_xml"
-            BIBTEX_FILE: "docs/assets/bibtex/create_mission_xml_literature.bib"
-          src-dirs: ../aircraft-design/create_mission_xml/src/
-          full-doc: true
+          src-dirs: aircraft-design/create_mission_xml/src
+          full-doc: True
+          doxy-cfg:
+            OUTPUT_DIRECTORY: "./docs/create_mission_xml"
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+            BIBTEX_FILE: docs/assets/bibtex/create_mission_xml_literature.bib
         fuselage_design:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "fuselage_design"
-            OUTPUT_DIR: "docs/api/fuselage_design"
-            BIBTEX_FILE: "docs/assets/bibtex/fuselage_design_literature.bib"
-          src-dirs: ../aircraft-design/fuselage_design/src/
+          src-dirs: aircraft-design/fuselage_design/src
           full-doc: true
+          doxy-cfg:
+            OUTPUT_DIRECTORY: "./docs/fuselage_design"
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
         wing_design:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "wing_design"
-            OUTPUT_DIR: "docs/api/wing_design"
-            BIBTEX_FILE: "docs/assets/bibtex/wing_design_literature.bib"
-          src-dirs: ../aircraft-design/wing_design/src/
+          src-dirs: aircraft-design/wing_design/src
           full-doc: True
+          doxy-cfg:
+            OUTPUT_DIRECTORY: "./docs/wing_design"
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
         empennage_design:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "empennage_design"
-            OUTPUT_DIR: "docs/api/empennage_design"
-          src-dirs: ../aircraft-design/empennage_design/src/
+          src-dirs: aircraft-design/empennage_design/src
           full-doc: true
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+            OUTPUT_DIRECTORY: "./docs/empennage_design"
         tank_design:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "tank_design"
-            OUTPUT_DIR: "docs/api/tank_design"
-          src-dirs: ../aircraft-design/tank_design/src/
+          src-dirs: aircraft-design/tank_design/src
           full-doc: true
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+            OUTPUT_DIRECTORY: "./docs/tank_design"
         landing_gear_design:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "landing_gear_design"
-            OUTPUT_DIR: "docs/api/landing_gear_design"
-          src-dirs: ../aircraft-design/landing_gear_design/src/
+          src-dirs: aircraft-design/landing_gear_design/src
           full-doc: true
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+            OUTPUT_DIRECTORY: "./docs/landing_gear_design"
         systems_design:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "systems_design"
-            OUTPUT_DIR: "docs/api/systems_design"
-          src-dirs: ../aircraft-design/systems_design/src/
+          src-dirs: aircraft-design/systems_design/src
+          full-doc: true
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+            OUTPUT_DIRECTORY: "./docs/systems_design"
+        ecological_assessment:
+          src-dirs: aircraft-design/ecological_assessment/src
           full-doc: true
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+            OUTPUT_DIRECTORY: "./docs/ecological_assessment"
+            BIBTEX_FILE: docs/assets/bibtex/ecological_assessment_literature.bib
         aerodynamic_analysis:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "aerodynamic_analysis"
-            OUTPUT_DIR: "docs/api/aerodynamic_analysis"
-          src-dirs: ../aircraft-design/aerodynamic_analysis/src/
+          src-dirs: aircraft-design/aerodynamic_analysis/src
           full-doc: true
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+            OUTPUT_DIRECTORY: "./docs/aerodynamic_analysis"
         aircraftGeometry2:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "aircraftGeometry2"
-            OUTPUT_DIR: "docs/api/aircraftGeometry2"
-          src-dirs: ../aircraft-design/libs/aircraftGeometry2/src/
+          src-dirs: aircraft-design/libs/aircraftGeometry2/src
           full-doc: true
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+            OUTPUT_DIRECTORY: "./docs/aircraftGeometry2"
         engine:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "engine"
-            OUTPUT_DIR: "docs/api/engine"
-          src-dirs: ../aircraft-design/libs/engine/src/
+          src-dirs: aircraft-design/libs/engine/src
           full-doc: true
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+            OUTPUT_DIRECTORY: "./docs/engine"
         mission_analysis:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "mission_analysis"
-            OUTPUT_DIR: "docs/api/mission_analysis"
-            BIBTEX_FILE: "docs/assets/bibtex/mission_analysis_literature.bib"
-          src-dirs: ../aircraft-design/mission_analysis/src/
+          src-dirs: aircraft-design/mission_analysis/src
           full-doc: true
-        weight_and_balance_analysis:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "weight_and_balance_analysis"
-            OUTPUT_DIR: "docs/api/weight_and_balance_analysis"
-          src-dirs: ../aircraft-design/weight_and_balance_analysis/src/
-          full-doc: true
-        performance_assesment:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "performance_assesment"
-            OUTPUT_DIR: "docs/api/performance_assesment"
-          src-dirs: ../aircraft-design/performance_assesment/src/
-          full-doc: true
-        cost_estimation:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "cost_estimation"
-            OUTPUT_DIR: "docs/api/cost_estimation"
-          src-dirs: ../aircraft-design/cost_estimation/src/
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+            OUTPUT_DIRECTORY: "./docs/mission_analysis"
+        constraint_analysis:
+          src-dirs: aircraft-design/constraint_analysis/src
           full-doc: true
-        aircraft_geometry2:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "aircraft_geometry2"
-            OUTPUT_DIR: "docs/api/aircraft_geometry2"
-          src-dirs: ../aircraft-design/libs/aircraftGeometry2/src/
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+            OUTPUT_DIRECTORY: "./docs/constraint_analysis"
+        performance_assessment:
+          src-dirs: aircraft-design/performance_assessment/src
           full-doc: true
-        engine:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "engine"
-            OUTPUT_DIR: "docs/api/engine"
-          src-dirs: ../aircraft-design/libs/engine/src/
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+            OUTPUT_DIRECTORY: "./docs/performance_assessment"
+        weight_and_balance_analysis:
+          src-dirs: aircraft-design/weight_and_balance_analysis/src
           full-doc: true
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+            OUTPUT_DIRECTORY: "./docs/weight_and_balance_analysis"
+
   - glightbox                             # Plugin for lightbox-style image and content viewing.
 
 # === Theme configuration ===
@@ -274,13 +274,18 @@ nav:                                      # Customizes the main navigation struc
             - Introduction: documentation/sizing/create_mission_xml/index.md
             - Getting Started: documentation/sizing/create_mission_xml/getting_started.md
             - Mission Steps: documentation/sizing/create_mission_xml/mission_steps.md
+            - API Reference:
+              - create_mission_xml/classes.md
+              - create_mission_xml/namespaces.md
+              - create_mission_xml/files.md
+              - create_mission_xml/functions.md
           - Fuselage Design:
             - Introduction: documentation/sizing/fuselage_design/index.md
             - Getting Started: documentation/sizing/fuselage_design/getting_started.md
             - Design Method: documentation/sizing/fuselage_design/design_method.md
             - Run your First Design: documentation/sizing/fuselage_design/run_your_first_design.md
             - Software Architecture: documentation/sizing/fuselage_design/software_architecture.md
-          # - API Reference: # TODO define for Python
+          #  # - API Reference: # TODO define for Python
           - Wing Design:
             - Introduction: documentation/sizing/wing_design/index.md
             - Getting Started: documentation/sizing/wing_design/getting-started.md
@@ -312,7 +317,6 @@ nav:                                      # Customizes the main navigation struc
             # - API Reference: # TODO define for Python
           - Propulsion Design:
             - Introduction: documentation/sizing/propulsion_design/index.md
-            - Overview: documentation/sizing/propulsion_design/overview.md
             - Getting Started: documentation/sizing/propulsion_design/getting-started.md
             - Engineering Principles: documentation/sizing/propulsion_design/engineering_principles.md
             - Software Architecture: documentation/sizing/propulsion_design/software_architecture.md
@@ -340,8 +344,8 @@ nav:                                      # Customizes the main navigation struc
               - systems_design/namespaces.md
               - systems_design/files.md
               - systems_design/functions.md
-      - Analysis:
-          - documentation/analysis/index.md # Link to analysis module page.
+      - Analysis:   
+          - Modules: documentation/analysis.md # Link to analysis module page.
           - Mission Analysis:
             - Introduction: documentation/analysis/mission_analysis/index.md
             - Getting Started: documentation/analysis/mission_analysis/getting_started.md
@@ -356,16 +360,7 @@ nav:                                      # Customizes the main navigation struc
             - Introduction: documentation/analysis/weight_and_balance_analysis/index.md
             - Basic Concepts: documentation/analysis/weight_and_balance_analysis/basic-concepts.md
             - Usage: documentation/analysis/weight_and_balance_analysis/usage.md
-            # - API Reference: # TODO define for Python
-          - Performance Assessment:
-            - Introduction: documentation/analysis/performance_assessment/index.md
-            - Getting Started: documentation/analysis/performance_assessment/getting_started.md
-            - Capabilities:
-              - Payload-Range Diagram: documentation/analysis/performance_assessment/payload_range_diagram.md
-              - Takeoff Performance: documentation/analysis/performance_assessment/takeoff_performance.md
-              - Landing Performance: documentation/analysis/performance_assessment/landing_performance.md
-              - Flight Envelope: documentation/analysis/performance_assessment/flight_envelope.md
-              - Ceiling Performance: documentation/analysis/performance_assessment/ceiling_performance.md
+          #  # - API Reference: # TODO define for Python
           - Cost Estimation:
             - Introduction: documentation/analysis/cost_estimation/index.md
             - Getting Started: documentation/analysis/cost_estimation/getting_started.md
@@ -388,33 +383,38 @@ nav:                                      # Customizes the main navigation struc
             - Introduction: documentation/analysis/aerodynamic_analysis/getting_started.md
             - Aerodynamic Principles: documentation/analysis/aerodynamic_analysis/aerodynamic_principles.md
             - Software Architecture: documentation/analysis/aerodynamic_analysis/software_architecture.md
+            - API Reference:
+              - aerodynamic_analysis/classes.md
+              - aerodynamic_analysis/namespaces.md
+              - aerodynamic_analysis/files.md
+              - aerodynamic_analysis/functions.md
           - Constraint Analysis:
             - Introduction: documentation/analysis/constraint_analysis/index.md
             - Principles: documentation/analysis/constraint_analysis/principles.md
+            - API Reference:
+              - constraint_analysis/classes.md
+              - constraint_analysis/namespaces.md
+              - constraint_analysis/files.md
+              - constraint_analysis/functions.md
+          - Performance Assessment:
+            - Introduction: documentation/analysis/performance_assessment/index.md
+            - Getting Started: documentation/analysis/performance_assessment/getting_started.md
+            - Mission Methods: documentation/analysis/performance_assessment/methods.md
+            - Mission Steps: documentation/analysis/performance_assessment/mission_steps.md
+            - API Reference:
+              - performance_assessment/classes.md
+              - performance_assessment/namespaces.md
+              - performance_assessment/files.md
+              - performance_assessment/functions.md
     - Libraries:
         - documentation/libraries/index.md # Link to libraries overview.
         - AircraftGeometry2:
           - Introduction: documentation/libraries/aircraftGeometry2/index.md
           - Getting Started: documentation/libraries/aircraftGeometry2/getting-started.md
-          - Tutorial:
-            - Overview: documentation/libraries/aircraftGeometry2/tutorial.md
-            - Geometry: documentation/libraries/aircraftGeometry2/tutorial-geometry.md
-            - Factory: documentation/libraries/aircraftGeometry2/tutorial-factory.md
-            - Convert: documentation/libraries/aircraftGeometry2/tutorial-convert.md
-          - API Reference:
-            - aircraftGeometry2/classes.md
-            - aircraftGeometry2/namespaces.md
-            - aircraftGeometry2/files.md
-            - aircraftGeometry2/functions.md
+          - Tutorial: documentation/libraries/aircraftGeometry2/tutorial.md
         - engine:
-          - Overview:
-            - documentation/libraries/engine/index.md
-          - API Reference:
-            - engine/classes.md
-            - engine/namespaces.md
-            - engine/files.md
-            - engine/functions.md
-    - Utilities: documentation/additional-software.md
+          - Introduction: documentation/libraries/engine/index.md 
+    - Utilities: documentation/additional_software.md
     - Workflow: 'workflow.md' # Link to the workflow page.
   - Get Involved:
     - Developer Guide: get-involved/developer-installation.md # Top-level item for contributions and development.
@@ -455,4 +455,4 @@ nav:                                      # Customizes the main navigation struc
       - About us: 'about.md'              # Link to the about page.
       - License: 'license.md'             # Link to license information.
       - Contact: 'contact.md'             # Link to contact page.
-      - Partners: 'partners.md'           # Link to partners page.
+      - Partners: 'partners.md'           # Link to partners page.
\ No newline at end of file