diff --git a/developer-doc/AddingAnAnalysis.txt b/developer-doc/AddingAnAnalysis.md
similarity index 100%
rename from developer-doc/AddingAnAnalysis.txt
rename to developer-doc/AddingAnAnalysis.md
diff --git a/developer-doc/Doxyfile b/developer-doc/Doxyfile
index e84b7da6cf5b46d21d6900422569e874d94fdcbe..094ce6b5957e1540e8ad8ad642fce9c2a8487731 100644
--- a/developer-doc/Doxyfile
+++ b/developer-doc/Doxyfile
@@ -754,24 +754,24 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ./Intro.txt \
-                         ./mdTemplate.txt \
-                         ./plmdIntro.txt \
-                         ./usingDoxygen.txt \
-                         ./parsing.txt \
-                         ./links-to-user-manual.txt \
-                         ./AddingAColvar.txt \
-                         ./AddingAFunction.txt \
-                         ./AddingACLTool.txt \
-                         ./AddingAnAnalysis.txt \
-                         ./AddingAMeasure.txt \
-                         ./AddingAMultColvar.txt \
-                         ./InstallationLayout.txt \
-                         ./AddingRegressionTests.txt \
-                         ./HowToContributeToPlumed.txt \
-                         ./intro-git.txt \
-                         ./plumedcheck.txt \
-                         ./CodeFormatting.txt
+INPUT                  = ./Intro.md \
+                         ./mdTemplate.md \
+                         ./plmdIntro.md \
+                         ./usingDoxygen.md \
+                         ./parsing.md \
+                         ./links-to-user-manual.md \
+                         ./AddingAColvar.md \
+                         ./AddingAFunction.md \
+                         ./AddingACLTool.md \
+                         ./AddingAnAnalysis.md \
+                         ./AddingAMeasure.md \
+                         ./AddingAMultColvar.md \
+                         ./InstallationLayout.md \
+                         ./AddingRegressionTests.md \
+                         ./HowToContributeToPlumed.md \
+                         ./intro-git.md \
+                         ./plumedcheck.md \
+                         ./CodeFormatting.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses