Fixed issue with "make install"

Before this fix, attempting to "make install" without "make" first
could result in corrupted path in the Plumed.inc/Plumed.cmake
files (the one used to patch MD codes). This resulted in linking
errors when trying to use "plumed patch --shared"

CHANGES/v2.0.txt

@@ -134,6 +134,7 @@ For users:
 - Fixed a few innocuous memory leaks.
 - Fixed reader for xyz files, that now correctly detects missing columns. Also a related regtest has
   been changed.
+- Several small fixes in documentation and log file.
 
 For developers:
 - Renamed Value.cpp to BiasValue.cpp
@@ -142,6 +143,12 @@ Unreleased changes (will be included in 2.0.5)
 ----------------------------------------------
 See <a href="http://github.com/plumed/plumed2/commits/v2.0">branch v2.0 on git repository</a>.
 
+For users:
+- Fixed an issue in Makefile that could results in problems when
+  typing "make install" before "make" and then patching an MD code
+  with --shared option (pointed out by Abhi Acharya).
+- Small fixes in documentation.
+
 */
 
 

src/lib/Makefile

@@ -188,10 +188,10 @@ Plumed.inc:
 	@echo Building Plumed.inc
 	@echo "PLUMED_RUNTIME_LOAD=" $(realpath $(OBJ_DYNAMIC_WRAPPER)) $(LIBS) $(LDFLAGS) > $@
 	@echo "PLUMED_STATIC_LOAD=" $(realpath $(OBJ_KERNEL)) $(realpath $(OBJ_WRAPPER)) $(LIBS) $(DYNAMIC_LIBS) $(LDFLAGS) >> $@
-	@echo "PLUMED_SHARED_LOAD=" $(realpath ./)/$(PLUMED_SHARED_OBJ) $(LIBS) $(LDFLAGS) >> $@
+	@echo "PLUMED_SHARED_LOAD=" $(realpath ./)libplumed.$(SOEXT) $(LIBS) $(LDFLAGS) >> $@
 	@echo "PLUMED_RUNTIME_DEPENDENCIES="   >> $@
 	@echo "PLUMED_STATIC_DEPENDENCIES=" $(realpath $(OBJ_KERNEL)) $(realpath $(OBJ_WRAPPER))  >> $@
-	@echo "PLUMED_SHARED_DEPENDENCIES=" $(realpath ./)/$(PLUMED_SHARED_OBJ)  >> $@
+	@echo "PLUMED_SHARED_DEPENDENCIES=" $(realpath ./)libplumed.$(SOEXT)  >> $@
 
 Plumed.inc.runtime: Plumed.inc
 	@echo Building Plumed.inc, runtime-linking version
@@ -212,10 +212,10 @@ Plumed.cmake:
 	@echo Building Plumed.cmake
 	@echo "set(PLUMED_RUNTIME_LOAD " $(realpath $(OBJ_DYNAMIC_WRAPPER)) $(LIBS) $(LDFLAGS)")" > $@
 	@echo "set(PLUMED_STATIC_LOAD " $(realpath $(OBJ_KERNEL)) $(realpath $(OBJ_WRAPPER)) $(LIBS) $(DYNAMIC_LIBS) $(LDFLAGS)")" >> $@
-	@echo "set(PLUMED_SHARED_LOAD " $(realpath ./)/$(PLUMED_SHARED_OBJ) $(LIBS) $(LDFLAGS)")" >> $@
+	@echo "set(PLUMED_SHARED_LOAD " $(realpath ./)libplumed.$(SOEXT) $(LIBS) $(LDFLAGS)")" >> $@
 	@echo "set(PLUMED_RUNTIME_DEPENDENCIES) "   >> $@
 	@echo "set(PLUMED_STATIC_DEPENDENCIES " $(realpath $(OBJ_KERNEL)) $(realpath $(OBJ_WRAPPER))")"  >> $@
-	@echo "set(PLUMED_SHARED_DEPENDENCIES " $(realpath ./)/$(PLUMED_SHARED_OBJ)")"  >> $@
+	@echo "set(PLUMED_SHARED_DEPENDENCIES " $(realpath ./)libplumed.$(SOEXT)")"  >> $@
 
 Plumed.cmake.runtime: Plumed.cmake
 	@echo Building Plumed.cmake, runtime-linking version