Merge branch 'v2.1' into v2.2

Conflicts:
	src/maketools/update-plumedroot.sh
	user-doc/Installation.txt

CHANGES/v2.1.txt

@@ -227,6 +227,9 @@ For users:
   Notice that this bug was present also in v2.0 but in a different form.
   More information here (\issue{162}), including a workaround that allows masses to be fixed
   without repatching.
+- When installing with PLUMED_LIBSUFFIX an underscore is used as separator instead of a dash.
+  E.g. `make install PLUMED_LIBSUFFIX=2.1` will result in an executable named `plumed_v2.1`.
+  This fix a potential problem (see \ref Installation).
 - 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.

src/maketools/update-plumedroot.sh

@@ -35,7 +35,7 @@ if test -n "$PLUMED_LIBSUFFIX" ; then
 # this will result in an error in a later version
 # now we fall back to the previous behavior
   PLUMED_LIBSUFFIX="${PLUMED_LIBSUFFIX:=}"
-  test -n "$PLUMED_LIBSUFFIX" && PLUMED_LIBSUFFIX="-${PLUMED_LIBSUFFIX}"
+  test -n "$PLUMED_LIBSUFFIX" && PLUMED_LIBSUFFIX="_${PLUMED_LIBSUFFIX}"
 fi
 
 PLUMED_PROGRAM_NAME="$(echo plumed | sed "${program_transform_name}")${PLUMED_LIBSUFFIX}"

user-doc/Installation.txt

@@ -349,18 +349,28 @@ the following things:
 As a final note, if you want to install several PLUMED versions without using modules then you
 should provide a different suffix and/or prefix at configure time:
 \verbatim
-> ./configure prefix=$HOME/opt --program-suffix=-2.2 --program-prefix=mpi-
+> ./configure prefix=$HOME/opt --program-suffix=_2.2 --program-prefix=mpi-
 > make install
 \endverbatim
-This will install a plumed executable named "mpi-plumed-2.2". All the other files will be renamed similarly,
-e.g. the PLUMED library will be loaded with "-lmpi-plumed-2.2" and the PLUMED header files
-will be included with "#include <mpi-plumed-2.2/tools/Vector.h>".
+This will install a plumed executable named "mpi-plumed_2.2". All the other files will be renamed similarly,
+e.g. the PLUMED library will be loaded with "-lmpi-plumed_2.2" and the PLUMED header files
+will be included with "#include <mpi-plumed_2.2/tools/Vector.h>".
 Notice that you can also use arbitrary scripts to edit the name of the executable
 with the option --program-transform-name=PROGRAM
 (see <a href="http://www.gnu.org/software/autoconf/manual/autoconf-2.69/html_node/Transformation-Examples.html#Transformation-Examples"> autoconf documentation </a> for more info).
 These options are useful if you
 do not want to set up modules, but we believe that using modules as described above is more flexible.
 
+\warning Avoid suffixes starting with a dash since they could clash with the fact that plumed reserved names with a `-something` appended
+for scripts used in cross compiling  (see below).
+As a consequence, by doing
+\verbatim
+> make install --program-suffix=-2
+> make install
+\endverbatim
+The second install would remove all the executables installed by the first install.
+Better using `make install --program-suffix=_2`.
+
 \section Patching Patching your MD code
 
 In case your MD code is not supporting PLUMED already, you should modify it.