Index: /issm/trunk/doxygen/createchtmldoc.sh
===================================================================
--- /issm/trunk/doxygen/createchtmldoc.sh	(revision 9308)
+++ /issm/trunk/doxygen/createchtmldoc.sh	(revision 9308)
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+#remove previous doc
+rm -rf chtml
+
+#Go to root directory, because doxygen seems to have a problem running otherwise.
+cd $ISSM_TIER
+
+#Symlink the doxygen configuration file to root dir.
+ln -s "$ISSM_TIER/doxygen/doc_c/doxygen.config" ./doxygen.config
+ln -s "$ISSM_TIER/doxygen/doc_c/doxygenissm.css" ./doxygenissm.css
+ln -s "$ISSM_TIER/doxygen/doc_c/layoutissm.xml" ./layoutissm.xml
+
+#Run doxygen
+$ISSM_TIER/externalpackages/doxygen/install/bin/doxygen doxygen.config
+
+#Erase symlink
+rm doxygen.config doxygenissm.css layoutissm.xml 
Index: /issm/trunk/doxygen/creatematlabhtmldoc.sh
===================================================================
--- /issm/trunk/doxygen/creatematlabhtmldoc.sh	(revision 9308)
+++ /issm/trunk/doxygen/creatematlabhtmldoc.sh	(revision 9308)
@@ -0,0 +1,29 @@
+#!/bin/bash
+
+#remove previous doc
+rm -rf "$ISSM_TIER/doxygen/doc_m/matlabhtml"
+
+#copy issm_template in m2html
+cd $ISSM_TIER/externalpackages/m2html/install/templates
+ln -s $ISSM_TIER/doxygen/doc_m/template_issm ./template_issm
+
+#go to the main directory
+cd $ISSM_TIER
+
+#launch matlab
+matlab -nodisplay << EOF
+
+	%Add m2html in path
+	addpath(genpath_ice([issmtier() '/externalpackages/m2html/install']));
+
+	%Here are the subdirectories we want to go through:
+	mfiles={'src/m'};
+
+	%run m2html, and dump the documentation in ISSM_TIER/doc/website/doc_m/matlabhtml
+	m2html('htmldir',[issmtier() '/doxygen/doc_m/matlabhtml'],'recursive','on','source','on',...
+	'syntaxHighlighting','on','globalHypertextLinks','on','global','on','template','template_issm',...
+	'graph','off','index','menu','mFiles',mfiles);
+EOF
+
+#remove soft link
+rm "$ISSM_TIER/externalpackages/m2html/install/templates/template_issm"
Index: sm/trunk/doxygen/doc_c/createchtmldoc.sh
===================================================================
--- /issm/trunk/doxygen/doc_c/createchtmldoc.sh	(revision 9307)
+++ 	(revision )
@@ -1,18 +1,0 @@
-#!/bin/bash
-
-#remove previous doc
-rm -rf chtml
-
-#Go to root directory, because doxygen seems to have a problem running otherwise.
-cd $ISSM_TIER
-
-#Symlink the doxygen configuration file to root dir.
-ln -s "$ISSM_DIR/website/doc_c/doxygen.config" ./doxygen.config
-ln -s "$ISSM_DIR/website/doc_c/doxygenissm.css" ./doxygenissm.css
-ln -s "$ISSM_DIR/website/doc_c/layoutissm.xml" ./layoutissm.xml
-
-#Run doxygen
-$ISSM_TIER/externalpackages/doxygen/install/bin/doxygen doxygen.config
-
-#Erase symlink
-rm doxygen.config doxygenissm.css layoutissm.xml 
Index: /issm/trunk/doxygen/doc_c/doxygen.config
===================================================================
--- /issm/trunk/doxygen/doc_c/doxygen.config	(revision 9307)
+++ /issm/trunk/doxygen/doc_c/doxygen.config	(revision 9308)
@@ -39,5 +39,5 @@
 # where doxygen was started. If left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       =  ../website/doc_c
+OUTPUT_DIRECTORY       =  ./doxygen/doc_c/
 
 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 
Index: sm/trunk/doxygen/doc_m/creatematlabhtmldoc.sh
===================================================================
--- /issm/trunk/doxygen/doc_m/creatematlabhtmldoc.sh	(revision 9307)
+++ 	(revision )
@@ -1,38 +1,0 @@
-#!/bin/bash
-
-#remove previous doc
-rm -rf "$ISSM_TIER/doc/website/doc_m/matlabhtml"
-
-#copy issm_template in m2html
-cd "$ISSM_TIER/externalpackages/m2html/install/templates"
-ln -s "$ISSM_TIER/../website/doc_m/template_issm" ./template_issm
-
-#go to the main directory
-cd $ISSM_TIER
-
-#launch matlab
-matlab -nodisplay << EOF
-	%get ISSM_TIER, brief name
-	[status,ISSM_TIER_BRIEF]=system('basename `pwd`');
-	ISSM_TIER_BRIEF=ISSM_TIER_BRIEF(1:end-1); %skip the \n character
-	if status~=0 | isempty(ISSM_TIER_BRIEF) | length(ISSM_TIER_BRIEF)==1,
-		error('startup error message: could not retrieve ISSM_TIER brief name');
-	end
-
-	%Add m2html in path
-	addpath(genpath_ice([ISSM_TIER '/externalpackages/m2html/install']));
-
-	cd ../
-
-	%Here are the subdirectories we want to go through:
-	mfiles={[ISSM_TIER_BRIEF '/src/m']};
-	%mfiles={[ISSM_TIER_BRIEF '/src/m/classes/public/plot']};
-
-	%run m2html, and dump the documentation in ISSM_TIER/doc/website/doc_m/matlabhtml
-	m2html('htmldir',[ISSM_TIER '/../website/doc_m/matlabhtml'],'recursive','on','source','on',...
-	'syntaxHighlighting','on','globalHypertextLinks','on','global','on','template','template_issm',...
-	'graph','on','index','menu','mFiles',mfiles);
-EOF
-
-#remove soft link
-rm "$ISSM_TIER/externalpackages/m2html/install/templates/template_issm"