diff --git a/src/bias/BiasExternal.cpp b/src/bias/External.cpp
similarity index 100%
rename from src/bias/BiasExternal.cpp
rename to src/bias/External.cpp
diff --git a/src/bias/BiasLWalls.cpp b/src/bias/LWalls.cpp
similarity index 100%
rename from src/bias/BiasLWalls.cpp
rename to src/bias/LWalls.cpp
diff --git a/src/bias/BiasMetaD.cpp b/src/bias/MetaD.cpp
similarity index 100%
rename from src/bias/BiasMetaD.cpp
rename to src/bias/MetaD.cpp
diff --git a/src/bias/BiasMovingRestraint.cpp b/src/bias/MovingRestraint.cpp
similarity index 100%
rename from src/bias/BiasMovingRestraint.cpp
rename to src/bias/MovingRestraint.cpp
diff --git a/src/bias/BiasRatchet.cpp b/src/bias/Ratchet.cpp
similarity index 100%
rename from src/bias/BiasRatchet.cpp
rename to src/bias/Ratchet.cpp
diff --git a/src/bias/BiasRestraint.cpp b/src/bias/Restraint.cpp
similarity index 100%
rename from src/bias/BiasRestraint.cpp
rename to src/bias/Restraint.cpp
diff --git a/src/bias/BiasUWalls.cpp b/src/bias/UWalls.cpp
similarity index 100%
rename from src/bias/BiasUWalls.cpp
rename to src/bias/UWalls.cpp
diff --git a/src/bias/BiasValue.cpp b/src/bias/Value.cpp
similarity index 100%
rename from src/bias/BiasValue.cpp
rename to src/bias/Value.cpp
diff --git a/src/cltools/CLToolDriver.cpp b/src/cltools/Driver.cpp
similarity index 100%
rename from src/cltools/CLToolDriver.cpp
rename to src/cltools/Driver.cpp
diff --git a/src/cltools/CLToolInfo.cpp b/src/cltools/Info.cpp
similarity index 100%
rename from src/cltools/CLToolInfo.cpp
rename to src/cltools/Info.cpp
diff --git a/src/cltools/CLToolManual.cpp b/src/cltools/Manual.cpp
similarity index 100%
rename from src/cltools/CLToolManual.cpp
rename to src/cltools/Manual.cpp
diff --git a/src/cltools/CLToolSimpleMD.cpp b/src/cltools/SimpleMD.cpp
similarity index 100%
rename from src/cltools/CLToolSimpleMD.cpp
rename to src/cltools/SimpleMD.cpp
diff --git a/src/cltools/CLToolTemplateGenerator.cpp b/src/cltools/TemplateGenerator.cpp
similarity index 100%
rename from src/cltools/CLToolTemplateGenerator.cpp
rename to src/cltools/TemplateGenerator.cpp
diff --git a/src/colvar/ColvarAngle.cpp b/src/colvar/Angle.cpp
similarity index 100%
rename from src/colvar/ColvarAngle.cpp
rename to src/colvar/Angle.cpp
diff --git a/src/colvar/ColvarContactMap.cpp b/src/colvar/ContactMap.cpp
similarity index 100%
rename from src/colvar/ColvarContactMap.cpp
rename to src/colvar/ContactMap.cpp
diff --git a/src/colvar/ColvarCoordination.cpp b/src/colvar/Coordination.cpp
similarity index 100%
rename from src/colvar/ColvarCoordination.cpp
rename to src/colvar/Coordination.cpp
diff --git a/src/colvar/ColvarDRMSD.cpp b/src/colvar/DRMSD.cpp
similarity index 100%
rename from src/colvar/ColvarDRMSD.cpp
rename to src/colvar/DRMSD.cpp
diff --git a/src/colvar/ColvarDipole.cpp b/src/colvar/Dipole.cpp
similarity index 100%
rename from src/colvar/ColvarDipole.cpp
rename to src/colvar/Dipole.cpp
diff --git a/src/colvar/ColvarDistance.cpp b/src/colvar/Distance.cpp
similarity index 100%
rename from src/colvar/ColvarDistance.cpp
rename to src/colvar/Distance.cpp
diff --git a/src/colvar/ColvarEnergy.cpp b/src/colvar/Energy.cpp
similarity index 100%
rename from src/colvar/ColvarEnergy.cpp
rename to src/colvar/Energy.cpp
diff --git a/src/colvar/ColvarGyration.cpp b/src/colvar/Gyration.cpp
similarity index 100%
rename from src/colvar/ColvarGyration.cpp
rename to src/colvar/Gyration.cpp
diff --git a/src/colvar/ColvarPathMSD.cpp b/src/colvar/PathMSD.cpp
similarity index 99%
rename from src/colvar/ColvarPathMSD.cpp
rename to src/colvar/PathMSD.cpp
index e574362adbb0bd5ae707463eb19a0fccb2099dbc..5ea9826ba33ec0a39bd4642ef10064856256ac22 100644
--- a/src/colvar/ColvarPathMSD.cpp
+++ b/src/colvar/PathMSD.cpp
@@ -19,7 +19,7 @@
    You should have received a copy of the GNU Lesser General Public License
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "ColvarPathMSDBase.h"
+#include "PathMSDBase.h"
 #include "core/PlumedMain.h"
 
 using namespace std;
diff --git a/src/colvar/ColvarPathMSDBase.cpp b/src/colvar/PathMSDBase.cpp
similarity index 99%
rename from src/colvar/ColvarPathMSDBase.cpp
rename to src/colvar/PathMSDBase.cpp
index 80b41fd6f1e7e6a572e11684e6292bbfae9c0d77..fb8a6315197b4994a9d16037acda802fad9c92d1 100644
--- a/src/colvar/ColvarPathMSDBase.cpp
+++ b/src/colvar/PathMSDBase.cpp
@@ -22,7 +22,7 @@
 #include <cmath>
 
 #include "Colvar.h"
-#include "ColvarPathMSDBase.h"
+#include "PathMSDBase.h"
 #include "ActionRegister.h"
 
 #include "core/PlumedMain.h"
diff --git a/src/colvar/ColvarPathMSDBase.h b/src/colvar/PathMSDBase.h
similarity index 96%
rename from src/colvar/ColvarPathMSDBase.h
rename to src/colvar/PathMSDBase.h
index 6fe8b70087d43b15401cdb99b4840b7ad6ef0a01..66eced1c0983364d1e679461de246cbce1faf525 100644
--- a/src/colvar/ColvarPathMSDBase.h
+++ b/src/colvar/PathMSDBase.h
@@ -19,8 +19,8 @@
    You should have received a copy of the GNU Lesser General Public License
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_colvar_ColvarPathMSDBase_h
-#define __PLUMED_colvar_ColvarPathMSDBase_h
+#ifndef __PLUMED_colvar_PathMSDBase_h
+#define __PLUMED_colvar_PathMSDBase_h
 
 #include <cmath>
 
diff --git a/src/colvar/ColvarPropertyMap.cpp b/src/colvar/PropertyMap.cpp
similarity index 99%
rename from src/colvar/ColvarPropertyMap.cpp
rename to src/colvar/PropertyMap.cpp
index f7caa594191f9862a3d93b5a209c8c4b9ae9386a..a096a24c62cc5122f68203b69e45d4b83f613314 100644
--- a/src/colvar/ColvarPropertyMap.cpp
+++ b/src/colvar/PropertyMap.cpp
@@ -19,7 +19,7 @@
    You should have received a copy of the GNU Lesser General Public License
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "ColvarPathMSDBase.h"
+#include "PathMSDBase.h"
 #include "core/PlumedMain.h"
 
 using namespace std;
diff --git a/src/colvar/ColvarRMSD.cpp b/src/colvar/RMSD.cpp
similarity index 100%
rename from src/colvar/ColvarRMSD.cpp
rename to src/colvar/RMSD.cpp
diff --git a/src/colvar/ColvarTemplate.cpp b/src/colvar/Template.cpp
similarity index 100%
rename from src/colvar/ColvarTemplate.cpp
rename to src/colvar/Template.cpp
diff --git a/src/colvar/ColvarTorsion.cpp b/src/colvar/Torsion.cpp
similarity index 100%
rename from src/colvar/ColvarTorsion.cpp
rename to src/colvar/Torsion.cpp
diff --git a/src/colvar/ColvarVolume.cpp b/src/colvar/Volume.cpp
similarity index 100%
rename from src/colvar/ColvarVolume.cpp
rename to src/colvar/Volume.cpp
diff --git a/src/function/FunctionCombine.cpp b/src/function/Combine.cpp
similarity index 100%
rename from src/function/FunctionCombine.cpp
rename to src/function/Combine.cpp
diff --git a/src/function/FunctionFuncPathMSD.cpp b/src/function/FuncPathMSD.cpp
similarity index 100%
rename from src/function/FunctionFuncPathMSD.cpp
rename to src/function/FuncPathMSD.cpp
diff --git a/src/function/FunctionMatheval.cpp b/src/function/Matheval.cpp
similarity index 100%
rename from src/function/FunctionMatheval.cpp
rename to src/function/Matheval.cpp
diff --git a/src/function/FunctionPiecewise.cpp b/src/function/Piecewise.cpp
similarity index 100%
rename from src/function/FunctionPiecewise.cpp
rename to src/function/Piecewise.cpp
diff --git a/src/function/FunctionSort.cpp b/src/function/Sort.cpp
similarity index 100%
rename from src/function/FunctionSort.cpp
rename to src/function/Sort.cpp
diff --git a/src/function/FunctionTarget.cpp b/src/function/Target.cpp
similarity index 100%
rename from src/function/FunctionTarget.cpp
rename to src/function/Target.cpp