now we have README.md as the main page

documents/.gitignore

@@ -0,0 +1,13 @@
+# Ignore everything
+*
+# But not these files...
+!kratos_doxyfile
+!py_filter.sh
+!README
+!kratos_small.png
+!.gitignore
+
+# ...even if they are in subdirectories
+!*/
+html/*
+latex/*

documents/kratos_doxyfile

@@ -32,13 +32,13 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = Kratos
+PROJECT_NAME           = 
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 7.0.x
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -51,7 +51,7 @@ PROJECT_BRIEF          = "KRATOS Multiphysics ("Kratos") is a framework for buil
 # pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
 # the logo to the output directory.
 
-PROJECT_LOGO           =
+PROJECT_LOGO           = kratos_small.png
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
 # into which the generated documentation will be written. If a relative path is
@@ -68,7 +68,7 @@ OUTPUT_DIRECTORY       = ../documents
 # performance problems for the file system.
 # The default value is: NO.
 
-CREATE_SUBDIRS         = NO
+CREATE_SUBDIRS         = YES
 
 # If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
 # characters to appear in the names of generated files. If set to NO, non-ASCII
@@ -525,7 +525,7 @@ INTERNAL_DOCS          = NO
 # and Mac users are advised to set this option to NO.
 # The default value is: system dependent.
 
-CASE_SENSE_NAMES       = YES
+CASE_SENSE_NAMES       = NO
 
 # If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
 # their full class and namespace scopes in the documentation. If set to YES, the
@@ -791,8 +791,9 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ../kratos \
-                         ../applications
+INPUT                  = ../kratos
+INPUT                  += ../applications
+INPUT                  += ../README.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
@@ -837,7 +838,8 @@ FILE_PATTERNS          = *.c \
                          *.f95 \
                          *.f03 \
                          *.f08 \
-                         *.f 
+                         *.f \
+                         *.md
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.
@@ -875,6 +877,7 @@ EXCLUDE_PATTERNS       += */cmake_modules/*
 EXCLUDE_PATTERNS       += */scripts/*
 EXCLUDE_PATTERNS       += */SuperLU_4.3/*
 EXCLUDE_PATTERNS       += */custom_external_libraries/*
+EXCLUDE_PATTERNS       += */README.md/*
 
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
@@ -968,7 +971,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE =
+USE_MDFILE_AS_MAINPAGE =  ../README.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing