Added possibility to mention issues and branches in Doxygen

\issue{123} to get #123 and a link at the github issue page

\branch{v2.1} to get v2.1 and a link at the github branch page

CHANGES/v2.1.txt

@@ -183,13 +183,13 @@ For users:
 - Fixed bug in \ref ENSEMBLE derivatives when more than 1 argument was provided
 - Fixed bug in \ref GHOST : virial is now computed correctly.
 - Fixed a serious bug in virial communicated from plumed to gromacs, for both gromacs versions 4.6 and 5.0.
-  See notes <a href="http://github.com/plumed/plumed2/issues/132"> here </a>
+  See \issue{132}.
   This fix requires gromacs to be repatched and could be very important if you run biased simulations in the NPT ensemble.
 - Fixed a bug in the virial computed with \ref FIT_TO_TEMPLATE when the reference pdb had center non located at the origin.
 - Fixed a bug in the the forces computed with \ref FIT_TO_TEMPLATE when used in combination with \ref COM, \ref CENTER, or \ref GHOST
 - Fixed a bug that could lead plumed to be stuck with domain decomposition in some extreme case (one domain with all atoms, other domains empty).
 - Fixed a bug when \ref COMBINE or \ref MATHEVAL are used with PERIODIC keyword. Now when PERIODIC keyword is used the result
-  of the calculation is brought within the periodicity domain. See <a href="http://github.com/plumed/plumed2/issues/139"> here </a>.
+  of the calculation is brought within the periodicity domain. See \issue{139}.
 - Fixed a bug related to \ref RANDOM_EXCHANGES followed by \ref INCLUDE
 - Fixed bug in derivatives of histogram bead with triangular kernels
 - Updated gromacs patch 4.5.5 to 4.5.7
@@ -209,7 +209,7 @@ For developers:
 - Allow external VMD plugins to be detected with --has-external-molfile. This
   is required to enable some regtest with amber files.
 - Added --dump-full-virial to \ref driver
-- Allow definition of variables where some of the components have derivatives and some haven't (issue #131).
+- Allow definition of variables where some of the components have derivatives and some haven't (\issue{131}).
 - Improved travis tests with more debug options.
 - Improved some regtest to check out-of-diagonal virial components
 - Improved make cppcheck options.
@@ -218,6 +218,6 @@ For developers:
 Unreleased changes (will be included in 2.1.4)
 ---------------------------------------------
 
-See <a href="http://github.com/plumed/plumed2/commits/v2.1">branch v2.1 on git repository</a>.
+See branch \branch{v2.1} on git repository.
 
 */

user-doc/Doxyfile

@@ -221,7 +221,9 @@ TAB_SIZE               = 8
 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"
+    endhidden="\htmlonly </div> </details> \endhtmlonly" \
+    issue{1}="<a href=\"http://github.com/plumed/plumed2/issues/\1\">#\1</a>" \
+    branch{1}="<a href=\"http://github.com/plumed/plumed2/commits/\1\">\1</a>"
 
 # 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"