Merge branch 'munster' into v2.1

[makedoc]

Conflicts:
	user-doc/figs/belfast-2-ala.png
	user-doc/figs/belfast-2-transition.png

(these figures were shrinked in both munster and cambridge branches)

user-doc/Colvar.txt

@@ -25,11 +25,11 @@ implement all these collective variables without implementing having an unmanigi
 \ref DISTANCES GROUPA=1 GROUPB=2-100 LESS_THAN={RATIONAL R_0=3}) there are more computationally efficient options available in plumed
 (e.g. \ref COORDINATION).  However, MultiColvars are worth investigating as they provide a flexible syntax for many quite-complex CVs.
 
-\subpage Group
-\subpage Colvar
-\subpage dists
-\subpage Function
-\subpage mcolv
+- \subpage Group
+- \subpage Colvar
+- \subpage dists
+- \subpage Function
+- \subpage mcolv
 
 \page Colvar CV Documentation
 

user-doc/Doxyfile

@@ -218,7 +218,10 @@ TAB_SIZE               = 8
 # "Side Effects:". You can put \n's in the value part of an alias to insert
 # newlines.
 
-ALIASES                =
+ALIASES                = \
+    hidden="\htmlonly <details> <summary> <b> To learn more </b> </summary> <div class=\"hidden\"> \endhtmlonly" \
+    hidden{1}="\htmlonly <details> <summary> <b> To learn more: \1 </b> </summary> <div class=\"hidden\"> \endhtmlonly" \
+    endhidden="\htmlonly </div> </details> \endhtmlonly"
 
 # This tag can be used to specify a number of word-keyword mappings (TCL only).
 # A mapping has the form "name=value". For example adding "class=itcl::class"

user-doc/go-doxygen

@@ -43,6 +43,9 @@ awk -v version=$(plumed --no-mpi info --version) '{
 mv $file.tmp $file
 done
 
+cat html/doxygen.css plumed.css > html/doxygen.css.tmp
+mv html/doxygen.css.tmp html/doxygen.css
+
 cd latex
 
 # this is a workaround for a problem on the linux workstation

user-doc/plumed.css

+.hidden {
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: grey;
+}