diff --git a/.gitignore b/.gitignore
index 56f5b760ba..5ea8fce35a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,5 @@
 # ignore html dir for github pages
-/doc/html
+/doc/generated
 
 *.so
 *.[oa]
diff --git a/Doxyfile b/Doxyfile
index c768dff65d..e0b045a019 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -51,7 +51,7 @@ PROJECT_LOGO           = data/pictures/penguin_icon.png
 # If a relative path is entered, it will be relative to the location
 # where doxygen was started. If left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = doc/html
+OUTPUT_DIRECTORY       = doc/generated
 
 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
 # 4096 sub-directories (in 2 levels) under the output directory of each output
@@ -828,7 +828,7 @@ GENERATE_HTML          = YES
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be
 # put in front of it. If left blank `html' will be used as the default path.
 
-HTML_OUTPUT            = docs
+HTML_OUTPUT            =
 
 # The HTML_FILE_EXTENSION tag can be used to specify the file extension for
 # each generated HTML page (for example: .htm,.php,.asp). If it is left blank
diff --git a/Makefile b/Makefile
index 7ee5a26a1b..ff963faecf 100644
--- a/Makefile
+++ b/Makefile
@@ -210,10 +210,6 @@ upload_ms ms.upload: ms
 #####
 #####
 
-doxygen:
-	mkdir -p dox
-	doxygen Doxyfile
-
 run_sitl :
 	$(PAPARAZZI_HOME)/var/$(AIRCRAFT)/sim/simsitl
 
@@ -282,4 +278,4 @@ run_tests:
 
 test: all replace_current_conf_xml run_tests restore_conf_xml
 
-.PHONY: all print_build_version clean cleanspaces ab_clean dist_clean distclean dist_clean_irreversible doxygen run_sitl install uninstall test replace_current_conf_xml run_tests restore_conf_xml
+.PHONY: all print_build_version clean cleanspaces ab_clean dist_clean distclean dist_clean_irreversible run_sitl install uninstall test replace_current_conf_xml run_tests restore_conf_xml