Merge branch 'v2.2'

CHANGES/v2.2.txt

@@ -146,10 +146,22 @@ For users:
 - When looking for a value outside the GRID now the error include the name of the responsible 
   collective variable
 - Numerical check in LatticeReduction made less picky.
+- Files are now flushed at the correct step. Before this fix, they were flushed at the step before the requested one
+  (e.g. with \ref FLUSH STRIDE=100 at step 99, 199, etc).
+- In \ref METAD, INTERVAL with periodic variables now report an error.
 - Added --disable-dependency-tracking to ./configure
 - \ref LOAD now works also when plumed is installed with a suffix.
+- Added `--md-root` option to `plumed patch` which allows it to be run from a directory different from the one
+  where the md code is located.
 
 For developers:
+- Added a make target `all_plus_doc` that builds both code and docs.
+- Added possibility to set a default location for plumed library in runtime binding.
+  If the plumed wrapped is compiled with `-D__PLUMED_DEFAULT_KERNEL=/path/libplumedKernel.so`,
+  then if the env var PLUMED_KERNEL is undefined or empty PLUMED will look in the path at compile time.
+- Tentative port files are now available <a href=\"http://github.com/plumed/ports">here</a>. They can be used to install PLUMED
+  using MacPorts.
+
 
 See branch \branch{v2.2} on git repository.
 

src/wrapper/Plumed.c

@@ -127,12 +127,15 @@ plumed_plumedmain_function_holder* plumed_kernel_register(const plumed_plumedmai
 #ifdef __PLUMED_DEFAULT_KERNEL
 /*
   This variable allows a default path for the kernel to be hardcoded.
-  Can be usedful for hardcoding the predefined plumed location
+  Can be useful for hardcoding the predefined plumed location
   still allowing the user to override this choice setting PLUMED_KERNEL.
   The path should be chosen at compile time adding e.g.
-  -D__PLUMED_DEFAULT_KERNEL=\"/opt/local/lib/libplumed.dylib\"
+  -D__PLUMED_DEFAULT_KERNEL=/opt/local/lib/libplumed.dylib
 */
-    if(! (path && (*path) )) path=__PLUMED_DEFAULT_KERNEL;
+/* This is required to add quotes */
+#define PLUMED_QUOTE_DIRECT(name) #name
+#define PLUMED_QUOTE(macro) PLUMED_QUOTE_DIRECT(macro)
+    if(! (path && (*path) )) path=PLUMED_QUOTE(__PLUMED_DEFAULT_KERNEL);
 #endif
     if(path && (*path)){
       fprintf(stderr,"+++ Loading the PLUMED kernel runtime +++\n");

user-doc/Installation.txt

@@ -40,6 +40,10 @@ in their official distribution. If your favorite MD code is available "PLUMED re
 you will have to compile PLUMED first, then (optionally) install it, then check the MD codes' manual to
 discover how to link it.
 
+If you are using a Mac, notice that we are providing tentative port files to install
+PLUMED with MacPorts. Follow the instructions <a href=\"http://github.com/plumed/ports">here</a>
+and report feedbacks on the mailing list.
+
 \section ConfiguringPlumed Configuring PLUMED
 
 The `./configure` command