diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in
index 27a62d20f3..43ac634f0a 100644
--- a/docs/Doxyfile.in
+++ b/docs/Doxyfile.in
@@ -308,6 +308,15 @@ EXTENSION_MAPPING      =
 
 MARKDOWN_SUPPORT       = YES
 
+# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up
+# to that level are automatically included in the table of contents, even if
+# they do not have an id attribute.
+# Note: This feature currently applies only to Markdown headings.
+# Minimum value: 0, maximum value: 99, default value: 0.
+# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
+
+TOC_INCLUDE_HEADINGS   = 0
+
 # When enabled doxygen tries to link words that correspond to documented
 # classes, or namespaces to their corresponding documentation. Such a link can
 # be prevented in individual cases by putting a % sign in front of the word or
@@ -786,8 +795,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = @CMAKE_SOURCE_DIR@/CONTRIBUTING.md \
-                         @CMAKE_SOURCE_DIR@/docs \
+INPUT                  = @CMAKE_SOURCE_DIR@/docs \
                          @CMAKE_SOURCE_DIR@/tests \
                          @CMAKE_SOURCE_DIR@/src/aktualizr_info \
                          @CMAKE_SOURCE_DIR@/src/aktualizr_primary \
@@ -812,7 +820,9 @@ INPUT                  = @CMAKE_SOURCE_DIR@/CONTRIBUTING.md \
                          @CMAKE_SOURCE_DIR@/src/libaktualizr/uptane \
                          @CMAKE_SOURCE_DIR@/src/libaktualizr/utilities \
                          @CMAKE_SOURCE_DIR@/src/load_tests \
-                         @CMAKE_SOURCE_DIR@/src/sota_tools
+                         @CMAKE_SOURCE_DIR@/src/sota_tools \
+                         @CMAKE_SOURCE_DIR@/CONTRIBUTING.md \
+                         @CMAKE_SOURCE_DIR@/CHANGELOG.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
@@ -834,8 +844,8 @@ INPUT_ENCODING         = UTF-8
 # If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
 # *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
 # *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
-# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f, *.for, *.tcl,
-# *.vhd, *.vhdl, *.ucf, *.qsf, *.as and *.js.
+# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f95, *.f03, *.f08,
+# *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf and *.qsf.
 
 FILE_PATTERNS          = *.c \
                          *.cc \
@@ -2430,6 +2440,11 @@ DIAFILE_DIRS           =
 
 PLANTUML_JAR_PATH      =
 
+# When using plantuml, the PLANTUML_CFG_FILE tag can be used to specify a
+# configuration file for plantuml.
+
+PLANTUML_CFG_FILE      =
+
 # When using plantuml, the specified paths are searched for files specified by
 # the !include statement in a plantuml block.