diff --git a/src/analysis/Analysis.cpp b/src/analysis/Analysis.cpp
index d427897d4aef73f703089695b5017c6d6a6aa26a..da39c2d6d0f4410819257da9cb6b9e2b84247fc8 100644
--- a/src/analysis/Analysis.cpp
+++ b/src/analysis/Analysis.cpp
@@ -25,6 +25,7 @@
 #include "core/ActionWithValue.h"
 #include "core/PlumedMain.h"
 #include "core/Atoms.h"
+#include "tools/IFile.h"
 
 namespace PLMD {
 namespace analysis {
diff --git a/src/analysis/Histogram.cpp b/src/analysis/Histogram.cpp
index 52dc930ce2e26e62a32f8835fd5fa08838461332..1e06b421ae8adc1d699cf0260ed191b9622ba453 100644
--- a/src/analysis/Histogram.cpp
+++ b/src/analysis/Histogram.cpp
@@ -23,6 +23,8 @@
 #include "core/ActionRegister.h"
 #include "tools/Grid.h"
 #include "tools/KernelFunctions.h"
+#include "tools/IFile.h"
+#include "tools/OFile.h"
 
 namespace PLMD{
 namespace analysis{
diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index 20439f4ada2500856d46b70ae88fafc398ef4bfd..a888f1c816cad1c74b01d79f7bdae4eb35b6f78a 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -42,6 +42,7 @@
 #include "tools/Stopwatch.h"
 #include "tools/Citations.h"
 #include "ExchangePatterns.h"
+#include "tools/IFile.h"
 
 using namespace std;
 
diff --git a/src/generic/Read.cpp b/src/generic/Read.cpp
index bfaca652a18b8b9606a11bfc25a2466625fa7f8a..e4af6ef9499767286e5659d4ab3ed0f60ecb4254 100644
--- a/src/generic/Read.cpp
+++ b/src/generic/Read.cpp
@@ -25,6 +25,7 @@
 #include "core/PlumedMain.h"
 #include "core/ActionSet.h"
 #include "core/Atoms.h"
+#include "tools/IFile.h"
 
 namespace PLMD{
 namespace generic{
diff --git a/src/tools/KernelFunctions.cpp b/src/tools/KernelFunctions.cpp
index a2c8211e1db94067c0110bc90336a670e1bb8f41..940f9eff3958de44ff0608e2d507ee7927c25825 100644
--- a/src/tools/KernelFunctions.cpp
+++ b/src/tools/KernelFunctions.cpp
@@ -20,6 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "KernelFunctions.h"
+#include "IFile.h"
 
 namespace PLMD {
 
diff --git a/src/tools/Log.h b/src/tools/Log.h
index b2c3a832200e0020b23d0f78f6409e87e6373548..e31aedcfa525606ff1e69b3c5efb57c98bcc7e64 100644
--- a/src/tools/Log.h
+++ b/src/tools/Log.h
@@ -22,7 +22,7 @@
 #ifndef __PLUMED_tools_Log_h
 #define __PLUMED_tools_Log_h
 
-#include "File.h"
+#include "OFile.h"
 
 namespace PLMD{
 
diff --git a/src/tools/OFile.h b/src/tools/OFile.h
index b7df1c0bedbe7ecb0facae80ca19c07f68537a22..821abe0e3d880681330c9f0315851c0b79243e2e 100644
--- a/src/tools/OFile.h
+++ b/src/tools/OFile.h
@@ -28,6 +28,8 @@
 
 namespace PLMD{
 
+class Value;
+
 /**
 \ingroup TOOLBOX
 Class for output files
diff --git a/src/tools/Tools.cpp b/src/tools/Tools.cpp
index aa3fb03d1cb2a8218ab2be2799e973b45f4b63b9..f7a12edb955545211839744b42d82fc5fd7e6ea6 100644
--- a/src/tools/Tools.cpp
+++ b/src/tools/Tools.cpp
@@ -23,7 +23,7 @@
 #include "Tools.h"
 #include "AtomNumber.h"
 #include "Exception.h"
-#include "File.h"
+#include "IFile.h"
 #include <cstring>
 #include <dirent.h>