diff --git a/CHANGES/v2.1.txt b/CHANGES/v2.1.txt
index f8462e8d7ae62b5dfba1d03c1aacc97d5b182cf8..a8ee9b17ad189851404c2b1b01694350fbb5621b 100644
--- a/CHANGES/v2.1.txt
+++ b/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 +218,12 @@ 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.
+
+For users:
+- Fixed erroneously reported message about MPI at the end of ./configure.
+- Changed warning message about undocumented components.
+- PLUMED now says in the log file if it was compiled from a dirty git repository.
+
 
 */
diff --git a/configure b/configure
index dd7a26ec687ac3d0053a2e423e804caa7708bb71..8e7929cf677436cddb7c51b895e8c652e7f40b4e 100755
--- a/configure
+++ b/configure
@@ -5609,7 +5609,6 @@ fi
 mpi_found=ko
 # optional libraries follow
 if test $mpi == true ; then
-  mpi_found=ok
 
     found=ko
     ac_fn_cxx_check_header_mongrel "$LINENO" "mpi.h" "ac_cv_header_mpi_h" "$ac_includes_default"
@@ -5632,6 +5631,9 @@ fi
 $as_echo "$as_me: WARNING: cannot enable __PLUMED_MPI" >&2;}
     fi
 
+  if test "x$ac_cv_func_MPI_Init" = xyes; then
+    mpi_found=ok
+  fi
 else
   mpi_found=ko
 fi
diff --git a/configure.ac b/configure.ac
index 5125466dee3ac8cfeba3c416bac01d93ef55aa1e..f2da8633f7cc6c78b0964eac59fca6f6f0e734fe 100644
--- a/configure.ac
+++ b/configure.ac
@@ -335,8 +335,10 @@ AC_CHECK_LIB([dl],dlopen, [STATIC_LIBS="-ldl $STATIC_LIBS"] [LIBS="-ldl $LIBS"])
 mpi_found=ko
 # optional libraries follow
 if test $mpi == true ; then
-  mpi_found=ok
   PLUMED_CHECK_PACKAGE([mpi.h],[MPI_Init],[__PLUMED_MPI])
+  if test "x$ac_cv_func_MPI_Init" = xyes; then
+    mpi_found=ok
+  fi
 else 
   mpi_found=ko
 fi
diff --git a/user-doc/Doxyfile b/user-doc/Doxyfile
index ad6c676a54b442f7c518039858ee27f139c8048a..0e09cc6d07f6d0432aa6230a6e1787056403a3f9 100644
--- a/user-doc/Doxyfile
+++ b/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"
diff --git a/user-doc/tutorials/cambridge.txt b/user-doc/tutorials/cambridge.txt
index bb3ff28e72527d1e744b942615a5494345997bdd..fa2df772ed3f7d291ac65ca69b4fb654b7cc8c3b 100644
--- a/user-doc/tutorials/cambridge.txt
+++ b/user-doc/tutorials/cambridge.txt
@@ -184,7 +184,7 @@ without further rescaling needed.
 
 We can plot the time evolution of the CVs along with the height of the Gaussian.
 
-\image html belfast-6-wtb6.pdf "Time evolution of the CVs and Gaussian height during the first 2.5 ns of a well-tempered metadynamics simulation with biasfactor equal to 6."
+\image html belfast-6-wtb6.png "Time evolution of the CVs and Gaussian height during the first 2.5 ns of a well-tempered metadynamics simulation with biasfactor equal to 6."
 
 The system is initialized in one of the local minimum where it starts accumulating bias.
 As the simulation progresses and the bias added grows, the Gaussian height is progressively reduced.