diff --git a/mkdocs.yml b/mkdocs.yml
index 0ce182f8fed87b7976cf1b4a65956a16bd0eb9dc..2f3c81d42885113b77b98abb3d3ab5b64d802221 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -143,6 +143,7 @@ plugins:
             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
         aerodynamic_analysis:
           variables:
@@ -168,6 +169,7 @@ plugins:
             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:
           variables:
@@ -277,6 +279,11 @@ nav:                                      # Customizes the main navigation struc
             - Getting Started: documentation/sizing/create_mission_xml/getting_started.md
             - Mission Steps: documentation/sizing/create_mission_xml/mission_steps.md
             - Airports: documentation/sizing/create_mission_xml/airports.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