diff --git a/openasip/bclib/saocl/oclhostsa.cc b/openasip/bclib/saocl/oclhostsa.cc
index cac1a30ab2..716bbb1276 100644
--- a/openasip/bclib/saocl/oclhostsa.cc
+++ b/openasip/bclib/saocl/oclhostsa.cc
@@ -32,10 +32,11 @@
 
 #define __STDC_LIMIT_MACROS
 
+#include <cassert>
+#include <climits>
+#include <cstdlib>
+
 #include "opencl_types.hh"
-#include <assert.h>
-#include <stdlib.h>
-#include <limits.h>
 
 //#define DEBUG_OCL_HOST
 
@@ -44,7 +45,9 @@
 #endif
 
 #include <CL/cl.h>
-#include <string.h>
+
+#include <cstring>
+
 #include "cl_tce.h"
 
 #define DUMMY_PLATFORM_ID 42
diff --git a/openasip/icdecoder_plugins/DefaultICDecoderPlugin.cc b/openasip/icdecoder_plugins/DefaultICDecoderPlugin.cc
index 3e9965e063..400f6b7f01 100644
--- a/openasip/icdecoder_plugins/DefaultICDecoderPlugin.cc
+++ b/openasip/icdecoder_plugins/DefaultICDecoderPlugin.cc
@@ -31,79 +31,72 @@
  * @note rating: red
  */
 
-#include <string>
-#include <vector>
-#include <set>
 #include <algorithm>
-#include <utility>
-#include <iterator>
+#include <cmath>
 #include <fstream>
 #include <iostream>
+#include <iterator>
 #include <map>
-#include <math.h>
-
-#include "boost/regex.hpp"
-#include "boost/format.hpp"
+#include <set>
+#include <string>
+#include <utility>
+#include <vector>
 
-#include "HDBManager.hh"
-#include "HDBRegistry.hh"
-#include "Machine.hh"
-#include "MachineInfo.hh"
-#include "Socket.hh"
+#include "Application.hh"
+#include "BinaryEncoding.hh"
+#include "BlockSourceCopier.hh"
 #include "Bus.hh"
-#include "Segment.hh"
+#include "CUOpcodeGenerator.hh"
 #include "ControlUnit.hh"
-#include "Guard.hh"
+#include "Conversion.hh"
+#include "DataObject.hh"
+#include "DefaultDecoderGenerator.hh"
+#include "DefaultICGenerator.hh"
+#include "DestinationField.hh"
+#include "Environment.hh"
+#include "ExecutionTrace.hh"
+#include "FUGuardEncoding.hh"
 #include "FUPort.hh"
-#include "RFPort.hh"
-#include "MachineImplementation.hh"
+#include "FUPortCode.hh"
+#include "GPRGuardEncoding.hh"
+#include "Guard.hh"
+#include "GuardEncoding.hh"
+#include "GuardField.hh"
+#include "HDBManager.hh"
+#include "HDBRegistry.hh"
 #include "ICDecoderEstimatorPlugin.hh"
-#include "Program.hh"
-#include "ExecutionTrace.hh"
-
 #include "ICDecoderGeneratorPlugin.hh"
-#include "ProGeTypes.hh"
-#include "NetlistBlock.hh"
+#include "IUPortCode.hh"
+#include "ImmediateControlField.hh"
+#include "ImmediateSlotField.hh"
+#include "LImmDstRegisterField.hh"
 #include "LoopBufferBlock.hh"
-#include "NetlistGenerator.hh"
+#include "Machine.hh"
+#include "MachineImplementation.hh"
+#include "MachineInfo.hh"
+#include "MapTools.hh"
+#include "MathTools.hh"
+#include "MoveSlot.hh"
 #include "Netlist.hh"
+#include "NetlistBlock.hh"
+#include "NetlistGenerator.hh"
 #include "NetlistPort.hh"
-#include "VHDLNetlistWriter.hh"
-#include "VerilogNetlistWriter.hh"
-#include "CUOpcodeGenerator.hh"
+#include "ProGeTypes.hh"
+#include "Program.hh"
+#include "RFPort.hh"
+#include "RFPortCode.hh"
+#include "RV32MicroCodeGenerator.hh"
+#include "Segment.hh"
 #include "SignalTypes.hh"
-
-#include "DefaultDecoderGenerator.hh"
-#include "DefaultICGenerator.hh"
-
-#include "BinaryEncoding.hh"
-#include "MoveSlot.hh"
+#include "Socket.hh"
+#include "SocketCodeTable.hh"
+#include "SocketEncoding.hh"
 #include "SourceField.hh"
-#include "DestinationField.hh"
-#include "GuardField.hh"
-#include "ImmediateSlotField.hh"
-#include "ImmediateControlField.hh"
-#include "LImmDstRegisterField.hh"
-#include "GuardEncoding.hh"
-#include "GPRGuardEncoding.hh"
-#include "FUGuardEncoding.hh"
 #include "UnconditionalGuardEncoding.hh"
-#include "SocketEncoding.hh"
-#include "RFPortCode.hh"
-#include "IUPortCode.hh"
-#include "FUPortCode.hh"
-#include "SocketCodeTable.hh"
-#include "BlockSourceCopier.hh"
-
-#include "Application.hh"
-#include "MathTools.hh"
-#include "DataObject.hh"
-#include "MapTools.hh"
-#include "Conversion.hh"
-#include "Environment.hh"
-#include "RV32MicroCodeGenerator.hh"
-
-#include "CUOpcodeGenerator.hh"
+#include "VHDLNetlistWriter.hh"
+#include "VerilogNetlistWriter.hh"
+#include "boost/format.hpp"
+#include "boost/regex.hpp"
 
 using namespace CostEstimator;
 using std::cerr;
diff --git a/openasip/opset/base/base.cc b/openasip/opset/base/base.cc
index 5464ca4483..76a1ceb676 100644
--- a/openasip/opset/base/base.cc
+++ b/openasip/opset/base/base.cc
@@ -31,9 +31,9 @@
  * @author Pekka Jääskeläinen 2005-2014 (pekka.jaaskelainen-no.spam-tut.fi)
  */
 
-#include <iostream>
+#include <cmath> // isnan()
 #include <fstream>
-#include <math.h> // isnan()
+#include <iostream>
 
 #include "OSAL.hh"
 #include "TCEString.hh"
@@ -41,6 +41,8 @@
 #include "Application.hh"
 #include "Conversion.hh"
 
+using namespace std;
+
 #define RUNTIME_ERROR_WITH_INT(MESSAGE, DATA) {\
        int len = strlen(MESSAGE) + 15;                \
        char *tmpBuf = static_cast<char*>(alloca(len));\
diff --git a/openasip/opset/base/double.cc b/openasip/opset/base/double.cc
index df352a6809..bb24a1c86f 100644
--- a/openasip/opset/base/double.cc
+++ b/openasip/opset/base/double.cc
@@ -31,9 +31,9 @@
  * @author Pekka Jääskeläinen 2005-2014 (pekka.jaaskelainen-no.spam-tut.fi)
  */
 
-#include <iostream>
+#include <cmath> // std::isnan()
 #include <fstream>
-#include <math.h> // isnan()
+#include <iostream>
 
 #include "OSAL.hh"
 #include "TCEString.hh"
@@ -41,6 +41,8 @@
 #include "Application.hh"
 #include "Conversion.hh"
 
+using namespace std;
+
 #define RUNTIME_ERROR_WITH_INT(MESSAGE, DATA) {\
        int len = strlen(MESSAGE) + 15;                \
        char *tmpBuf = static_cast<char*>(alloca(len));\
diff --git a/openasip/src/applibs/ImplementationTester/FUTestbenchGenerator.cc b/openasip/src/applibs/ImplementationTester/FUTestbenchGenerator.cc
index aad425deba..23dd2948d6 100644
--- a/openasip/src/applibs/ImplementationTester/FUTestbenchGenerator.cc
+++ b/openasip/src/applibs/ImplementationTester/FUTestbenchGenerator.cc
@@ -31,30 +31,32 @@
  * @note rating: red
  */
 
-#include <string>
-#include <sstream>
-#include <vector>
-#include <boost/random.hpp>
+#include "FUTestbenchGenerator.hh"
+
 #include <boost/nondet_random.hpp>
+#include <boost/random.hpp>
+#include <cstdint>
 #include <ctime>
-#include <stdint.h>
-#include "HDBManager.hh"
-#include "FUEntry.hh"
-#include "TestbenchGenerator.hh"
-#include "FUTestbenchGenerator.hh"
+#include <sstream>
+#include <string>
+#include <vector>
+
+#include "Conversion.hh"
 #include "FUArchitecture.hh"
+#include "FUEntry.hh"
+#include "FUImplementation.hh"
+#include "FUPortImplementation.hh"
 #include "FunctionUnit.hh"
+#include "HDBManager.hh"
+#include "HWOperation.hh"
+#include "InputPortState.hh"
 #include "Machine.hh"
 #include "MachineState.hh"
 #include "MachineStateBuilder.hh"
 #include "MemorySystem.hh"
 #include "OutputPortState.hh"
-#include "InputPortState.hh"
-#include "FUPortImplementation.hh"
-#include "FUImplementation.hh"
-#include "HWOperation.hh"
 #include "StringTools.hh"
-#include "Conversion.hh"
+#include "TestbenchGenerator.hh"
 
 using std::string;
 using std::vector;
diff --git a/openasip/src/applibs/ImplementationTester/ImplementationTester.cc b/openasip/src/applibs/ImplementationTester/ImplementationTester.cc
index 7beb0f4acb..282ae48927 100644
--- a/openasip/src/applibs/ImplementationTester/ImplementationTester.cc
+++ b/openasip/src/applibs/ImplementationTester/ImplementationTester.cc
@@ -30,39 +30,38 @@
  * @author Otto Esko 2010 (otto.esko-no.spam-tut.fi)
  * @note rating: red
  */
-#include <iostream>
+#include "ImplementationTester.hh"
+
+#include <cstdint>
 #include <cstdlib>
-#include <iostream>
 #include <fstream>
-#include <string>
+#include <iostream>
+#include <map>
 #include <sstream>
-#include <fstream>
+#include <string>
 #include <vector>
-#include <map>
-#include <stdint.h>
 
-#include "ImplementationTester.hh"
-#include "HDBManager.hh"
 #include "CachedHDBManager.hh"
-#include "FUEntry.hh"
 #include "FUArchitecture.hh"
+#include "FUEntry.hh"
 #include "FUImplementation.hh"
-#include "RFEntry.hh"
-#include "RFArchitecture.hh"
-#include "RFImplementation.hh"
+#include "FUTestbenchGenerator.hh"
 #include "FunctionUnit.hh"
+#include "GhdlSimulator.hh"
+#include "HDBManager.hh"
+#include "HWBlockImplementation.hh"
+#include "ImplementationSimulator.hh"
+#include "InputPortState.hh"
 #include "Machine.hh"
 #include "MachineState.hh"
 #include "MachineStateBuilder.hh"
 #include "MemorySystem.hh"
+#include "ModelsimSimulator.hh"
 #include "OutputPortState.hh"
-#include "InputPortState.hh"
-#include "FUTestbenchGenerator.hh"
+#include "RFArchitecture.hh"
+#include "RFEntry.hh"
+#include "RFImplementation.hh"
 #include "RFTestbenchGenerator.hh"
-#include "ImplementationSimulator.hh"
-#include "GhdlSimulator.hh"
-#include "ModelsimSimulator.hh"
-#include "HWBlockImplementation.hh"
 
 using std::string;
 using std::vector;
diff --git a/openasip/src/applibs/ImplementationTester/RFTestbenchGenerator.cc b/openasip/src/applibs/ImplementationTester/RFTestbenchGenerator.cc
index 4ec1915e5d..68ccfd72e2 100644
--- a/openasip/src/applibs/ImplementationTester/RFTestbenchGenerator.cc
+++ b/openasip/src/applibs/ImplementationTester/RFTestbenchGenerator.cc
@@ -30,26 +30,28 @@
  * @note rating: red
  */
 
-#include <string>
-#include <sstream>
-#include <vector>
-#include <boost/random.hpp>
+#include "RFTestbenchGenerator.hh"
+
 #include <boost/nondet_random.hpp>
+#include <boost/random.hpp>
+#include <cstdint>
 #include <ctime>
-#include <stdint.h>
+#include <sstream>
+#include <string>
+#include <vector>
+
 #include "HDBManager.hh"
-#include "RFEntry.hh"
-#include "TestbenchGenerator.hh"
-#include "RFTestbenchGenerator.hh"
-#include "RFArchitecture.hh"
 #include "Machine.hh"
 #include "MachineState.hh"
 #include "MachineStateBuilder.hh"
+#include "MathTools.hh"
 #include "MemorySystem.hh"
-#include "RegisterFileState.hh"
-#include "RFPortImplementation.hh"
+#include "RFArchitecture.hh"
+#include "RFEntry.hh"
 #include "RFImplementation.hh"
-#include "MathTools.hh"
+#include "RFPortImplementation.hh"
+#include "RegisterFileState.hh"
+#include "TestbenchGenerator.hh"
 
 using std::string;
 using std::vector;
diff --git a/openasip/src/applibs/ImplementationTester/TestbenchGenerator.cc b/openasip/src/applibs/ImplementationTester/TestbenchGenerator.cc
index 8f95aee01d..11d4fd4c2b 100644
--- a/openasip/src/applibs/ImplementationTester/TestbenchGenerator.cc
+++ b/openasip/src/applibs/ImplementationTester/TestbenchGenerator.cc
@@ -30,19 +30,21 @@
  * @note rating: red
  */
 
-#include <string>
-#include <sstream>
+#include "TestbenchGenerator.hh"
+
+#include <boost/format.hpp>
+#include <cstdint>
 #include <fstream>
-#include <vector>
 #include <map>
-#include <stdint.h>
-#include <boost/format.hpp>
-#include "TestbenchGenerator.hh"
-#include "StringTools.hh"
+#include <sstream>
+#include <string>
+#include <vector>
+
+#include "Conversion.hh"
 #include "Environment.hh"
 #include "FileSystem.hh"
-#include "Conversion.hh"
 #include "HWBlockImplementation.hh"
+#include "StringTools.hh"
 
 using std::string;
 using std::vector;
diff --git a/openasip/src/applibs/LLVMBackend/LLVMTCEIRBuilder.cc b/openasip/src/applibs/LLVMBackend/LLVMTCEIRBuilder.cc
index 01aebcb840..62fc9a896a 100644
--- a/openasip/src/applibs/LLVMBackend/LLVMTCEIRBuilder.cc
+++ b/openasip/src/applibs/LLVMBackend/LLVMTCEIRBuilder.cc
@@ -38,48 +38,49 @@
 #include "CompilerWarnings.hh"
 IGNORE_COMPILER_WARNING("-Wunused-parameter")
 
-#include "LLVMTCEIRBuilder.hh"
-#include "ControlFlowGraph.hh"
-#include "Procedure.hh"
+#include <llvm/ADT/SmallString.h>
+#include <llvm/CodeGen/MachineJumpTableInfo.h>
+#include <llvm/CodeGen/MachineMemOperand.h>
+#include <llvm/IR/Value.h>
+#include <llvm/MC/MCContext.h>
+#include <llvm/MC/MCSymbol.h>
+
+#include <cstdlib>
+
+#include "AbsoluteToRelativeJumps.hh"
 #include "AddressSpace.hh"
-#include "ControlUnit.hh"
-#include "DataDependenceGraph.hh"
-#include "TerminalBasicBlockReference.hh"
-#include "TerminalSymbolReference.hh"
-#include "TerminalFUPort.hh"
-#include "SequentialScheduler.hh"
-#include "PreOptimizer.hh"
 #include "BBSchedulerController.hh"
-#include "CycleLookBackSoftwareBypasser.hh"
+#include "BasicBlock.hh"
+#include "CallsToJumps.hh"
+#include "ControlFlowGraph.hh"
+#include "ControlUnit.hh"
 #include "CopyingDelaySlotFiller.hh"
-#include "SimpleIfConverter.hh"
-#include "Peel2BBLoops.hh"
-#include "passes/InnerLoopFinder.hh"
-#include "Machine.hh"
-#include "InstructionReferenceManager.hh"
-#include "Program.hh"
-#include "RegisterCopyAdder.hh"
-#include "LLVMTCECmdLineOptions.hh"
-#include "Instruction.hh"
+#include "CycleLookBackSoftwareBypasser.hh"
+#include "DataDependenceGraph.hh"
+#include "FUPort.hh"
 #include "FunctionUnit.hh"
 #include "HWOperation.hh"
-#include "FUPort.hh"
-#include "BasicBlock.hh"
-#include "Move.hh"
+#include "Instruction.hh"
+#include "InstructionReferenceManager.hh"
+#include "LLVMTCECmdLineOptions.hh"
+#include "LLVMTCEIRBuilder.hh"
+#include "Machine.hh"
 #include "MapTools.hh"
+#include "Move.hh"
 #include "PRegionMarkerAnalyzer.hh"
+#include "Peel2BBLoops.hh"
 #include "PostpassOperandSharer.hh"
-#include "CallsToJumps.hh"
-#include "AbsoluteToRelativeJumps.hh"
-
-#include <stdlib.h>
-#include <llvm/ADT/SmallString.h>
-#include <llvm/MC/MCContext.h>
-#include <llvm/MC/MCSymbol.h>
-#include <llvm/CodeGen/MachineJumpTableInfo.h>
-#include <llvm/IR/Value.h>
-#include <llvm/CodeGen/MachineMemOperand.h>
+#include "PreOptimizer.hh"
+#include "Procedure.hh"
+#include "Program.hh"
+#include "RegisterCopyAdder.hh"
+#include "SequentialScheduler.hh"
+#include "SimpleIfConverter.hh"
+#include "TerminalBasicBlockReference.hh"
+#include "TerminalFUPort.hh"
+#include "TerminalSymbolReference.hh"
 #include "llvm/Analysis/AliasAnalysis.h"
+#include "passes/InnerLoopFinder.hh"
 
 POP_COMPILER_DIAGS
 
diff --git a/openasip/src/applibs/LLVMBackend/plugin/TCEISelLowering.cc b/openasip/src/applibs/LLVMBackend/plugin/TCEISelLowering.cc
index 935940b28b..1631694c33 100644
--- a/openasip/src/applibs/LLVMBackend/plugin/TCEISelLowering.cc
+++ b/openasip/src/applibs/LLVMBackend/plugin/TCEISelLowering.cc
@@ -32,23 +32,24 @@
  * @author Heikki Kultala 2011-2012 (heikki.kultala-no.spam-tut.fi)
  */
 
-#include <assert.h>
-#include <string>
-#include "tce_config.h"
-#include <llvm/IR/Function.h>
-#include <llvm/IR/DerivedTypes.h>
-#include <llvm/IR/Intrinsics.h>
-#include <llvm/IR/CallingConv.h>
-#include <llvm/CodeGen/TargetLowering.h>
 #include <llvm/CodeGen/CallingConvLower.h>
-#include <llvm/CodeGen/SelectionDAG.h>
 #include <llvm/CodeGen/MachineFrameInfo.h>
-#include <llvm/CodeGen/MachineRegisterInfo.h>
 #include <llvm/CodeGen/MachineInstrBuilder.h>
+#include <llvm/CodeGen/MachineRegisterInfo.h>
+#include <llvm/CodeGen/SelectionDAG.h>
+#include <llvm/CodeGen/TargetLowering.h>
+#include <llvm/IR/CallingConv.h>
+#include <llvm/IR/DerivedTypes.h>
+#include <llvm/IR/Function.h>
+#include <llvm/IR/Intrinsics.h>
 #include <llvm/Support/raw_ostream.h>
-
 #include <llvm/Target/TargetLoweringObjectFile.h>
 
+#include <cassert>
+#include <string>
+
+#include "tce_config.h"
+
 //#include <llvm/Config/config.h>
 
 #include "TCEPlugin.hh"
diff --git a/openasip/src/applibs/LLVMBackend/plugin/TCERegisterInfo.cc b/openasip/src/applibs/LLVMBackend/plugin/TCERegisterInfo.cc
index d56f3129cf..ee16470d64 100644
--- a/openasip/src/applibs/LLVMBackend/plugin/TCERegisterInfo.cc
+++ b/openasip/src/applibs/LLVMBackend/plugin/TCERegisterInfo.cc
@@ -31,27 +31,27 @@
  * @author Heikki Kultala 2011-2016 (heikki.kultala-no.spam-tut.fi)
  */
 
-#include <assert.h>
-#include "tce_config.h"
-#include <llvm/IR/Type.h>
-#include <llvm/IR/Function.h>
-#include <llvm/CodeGen/MachineInstrBuilder.h>
+#include "TCERegisterInfo.hh"
+
+#include <llvm/ADT/STLExtras.h>
 #include <llvm/CodeGen/MachineFrameInfo.h>
+#include <llvm/CodeGen/MachineInstrBuilder.h>
+#include <llvm/CodeGen/RegisterScavenging.h>
 #include <llvm/CodeGen/TargetInstrInfo.h>
+#include <llvm/IR/Function.h>
+#include <llvm/IR/Type.h>
 #include <llvm/Target/TargetOptions.h>
 
-#include <llvm/ADT/STLExtras.h>
-#include <llvm/CodeGen/RegisterScavenging.h>
+#include <cassert>
 
-#include "TCEPlugin.hh"
-#include "TCERegisterInfo.hh"
-#include "TCETargetMachine.hh"
+#include "Application.hh"
+#include "Exception.hh"
+#include "LLVMTCECmdLineOptions.hh"
 #include "TCEInstrInfo.hh"
+#include "TCEPlugin.hh"
 #include "TCEString.hh"
-#include "Application.hh"
+#include "TCETargetMachine.hh"
 #include "tce_config.h"
-#include "LLVMTCECmdLineOptions.hh"
-#include "Exception.hh"
 
 using namespace llvm;
 
diff --git a/openasip/src/applibs/Scheduler/Algorithms/CopyingDelaySlotFiller.hh b/openasip/src/applibs/Scheduler/Algorithms/CopyingDelaySlotFiller.hh
index d563fbdf42..beb5ae8b77 100644
--- a/openasip/src/applibs/Scheduler/Algorithms/CopyingDelaySlotFiller.hh
+++ b/openasip/src/applibs/Scheduler/Algorithms/CopyingDelaySlotFiller.hh
@@ -33,14 +33,16 @@
 #ifndef COPYING_DELAY_SLOT_FILLER_HH
 #define COPYING_DELAY_SLOT_FILLER_HH
 
+#include <list>
 #include <map>
 #include <vector>
-#include <list>
-#include "Exception.hh"
-#include "ProgramOperation.hh"
+
+#include "Bus.hh"
+#include "ControlFlowEdge.hh"
 #include "ControlFlowGraph.hh"
 #include "DataDependenceGraph.hh"
-#include "ControlFlowEdge.hh"
+#include "Exception.hh"
+#include "ProgramOperation.hh"
 
 class BasicBlockNode;
 class ControlFlowGraph;
diff --git a/openasip/src/applibs/wxToolkit/MachineWindow/EditPart.cc b/openasip/src/applibs/wxToolkit/MachineWindow/EditPart.cc
index e92f764d74..242851b8ed 100644
--- a/openasip/src/applibs/wxToolkit/MachineWindow/EditPart.cc
+++ b/openasip/src/applibs/wxToolkit/MachineWindow/EditPart.cc
@@ -32,22 +32,24 @@
  * @note reviewed Jul 13 2004 by vpj, ll, jn, am
  */
 
-#include <wx/wx.h>
+#include "EditPart.hh"
+
+#include <math.h>
 #include <wx/cmdproc.h>
-#include <stdlib.h>
+#include <wx/wx.h>
+
+#include <cstdlib>
 #include <limits>
-#include <math.h>
 
 #include "Application.hh"
+#include "ComponentCommand.hh"
 #include "ContainerTools.hh"
+#include "EditPolicy.hh"
+#include "Figure.hh"
 #include "MachinePart.hh"
 #include "Port.hh"
-#include "Segment.hh"
-#include "EditPart.hh"
-#include "Figure.hh"
-#include "EditPolicy.hh"
 #include "Request.hh"
-#include "ComponentCommand.hh"
+#include "Segment.hh"
 
 using std::vector;
 using std::set;
diff --git a/openasip/src/base/mach/OperationTriggeredFormat.cc b/openasip/src/base/mach/OperationTriggeredFormat.cc
index 47fad81b30..79701f4594 100644
--- a/openasip/src/base/mach/OperationTriggeredFormat.cc
+++ b/openasip/src/base/mach/OperationTriggeredFormat.cc
@@ -30,13 +30,14 @@
  * @note rating: red
  */
 
-#include <stdio.h>
-
 #include "OperationTriggeredFormat.hh"
-#include "OperationTriggeredOperand.hh"
+
+#include <cstdio>
+
 #include "MOMTextGenerator.hh"
-#include "ObjectState.hh"
 #include "Machine.hh"
+#include "ObjectState.hh"
+#include "OperationTriggeredOperand.hh"
 
 namespace TTAMachine {
 
diff --git a/openasip/src/base/memory/RemoteMemory.cc b/openasip/src/base/memory/RemoteMemory.cc
index a49190b9b2..8f2488d957 100644
--- a/openasip/src/base/memory/RemoteMemory.cc
+++ b/openasip/src/base/memory/RemoteMemory.cc
@@ -28,9 +28,10 @@
  * @author Kalle Raiskila 2014
  */
 
-#include <assert.h>
 #include "RemoteMemory.hh"
 
+#include <cassert>
+
 typedef MinimumAddressableUnit MAU;
 
 void
diff --git a/openasip/src/bintools/Compiler/tceopgen/ExtensionGen.cc b/openasip/src/bintools/Compiler/tceopgen/ExtensionGen.cc
index 2c0d9da36a..2db70bea2d 100644
--- a/openasip/src/bintools/Compiler/tceopgen/ExtensionGen.cc
+++ b/openasip/src/bintools/Compiler/tceopgen/ExtensionGen.cc
@@ -30,21 +30,20 @@
  * @note rating: red
  */
 
-#include <iostream>
+#include <boost/format.hpp>
+#include <cassert>
 #include <fstream>
+#include <iostream>
 #include <set>
-#include <assert.h>
-#include <boost/format.hpp>
 
-#include "OperationPool.hh"
-#include "Operation.hh"
 #include "Conversion.hh"
-#include "OperationIndex.hh"
-#include "Operand.hh"
+#include "HWOperation.hh"
 #include "Machine.hh"
+#include "Operand.hh"
+#include "Operation.hh"
+#include "OperationIndex.hh"
+#include "OperationPool.hh"
 #include "StringTools.hh"
-#include "HWOperation.hh"
-
 
 /**
  * Returns a C type string for the given operand type.
diff --git a/openasip/src/bintools/Compiler/tceopgen/tceopgen.cc b/openasip/src/bintools/Compiler/tceopgen/tceopgen.cc
index f9862f8409..56cc24d6f8 100644
--- a/openasip/src/bintools/Compiler/tceopgen/tceopgen.cc
+++ b/openasip/src/bintools/Compiler/tceopgen/tceopgen.cc
@@ -30,17 +30,17 @@
  * @note rating: red
  */
 
-#include <iostream>
+#include <cassert>
 #include <fstream>
+#include <iostream>
 #include <set>
-#include <assert.h>
 
-#include "OperationPool.hh"
-#include "Operation.hh"
+#include "Application.hh"
 #include "Conversion.hh"
-#include "OperationIndex.hh"
 #include "Operand.hh"
-#include "Application.hh"
+#include "Operation.hh"
+#include "OperationIndex.hh"
+#include "OperationPool.hh"
 
 enum mode { NORMAL, FU_ADDRESSABLE, ADDRESSPACE, RISCV };
 /**
diff --git a/openasip/src/procgen/HDBEditor/HDBToHtml.cc b/openasip/src/procgen/HDBEditor/HDBToHtml.cc
index e21e3c84fa..32c8963c4d 100644
--- a/openasip/src/procgen/HDBEditor/HDBToHtml.cc
+++ b/openasip/src/procgen/HDBEditor/HDBToHtml.cc
@@ -31,32 +31,31 @@
  * @note rating: red
  */
 
-#include <time.h>
-
 #include "HDBToHtml.hh"
 
-#include "ContainerTools.hh"
+#include <ctime>
 
-#include "FUEntry.hh"
+#include "BlockImplementationFile.hh"
+#include "ContainerTools.hh"
+#include "CostEstimationData.hh"
+#include "CostFunctionPlugin.hh"
+#include "DataObject.hh"
+#include "ExecutionPipeline.hh"
 #include "FUArchitecture.hh"
+#include "FUEntry.hh"
+#include "FUExternalPort.hh"
 #include "FUImplementation.hh"
-#include "FunctionUnit.hh"
 #include "FUPort.hh"
+#include "FUPortImplementation.hh"
+#include "FunctionUnit.hh"
+#include "HDBManager.hh"
 #include "HWOperation.hh"
-#include "ExecutionPipeline.hh"
 #include "PipelineElement.hh"
-#include "FUExternalPort.hh"
-#include "RFExternalPort.hh"
-#include "FUPortImplementation.hh"
-#include "BlockImplementationFile.hh"
-#include "RFEntry.hh"
 #include "RFArchitecture.hh"
+#include "RFEntry.hh"
+#include "RFExternalPort.hh"
 #include "RFImplementation.hh"
 #include "RFPortImplementation.hh"
-#include "HDBManager.hh"
-#include "CostEstimationData.hh"
-#include "DataObject.hh"
-#include "CostFunctionPlugin.hh"
 
 using namespace TTAMachine;
 using namespace HDB;
diff --git a/openasip/src/procgen/MachInfo/MachInfo.cc b/openasip/src/procgen/MachInfo/MachInfo.cc
index b401f35cf0..9f33db441f 100644
--- a/openasip/src/procgen/MachInfo/MachInfo.cc
+++ b/openasip/src/procgen/MachInfo/MachInfo.cc
@@ -30,18 +30,18 @@
  * @author Pekka Jääskeläinen 2014
  */
 
-#include "Machine.hh"
+#include <cstdlib>
+#include <fstream>
+#include <iostream>
+
 #include "ControlUnit.hh"
-#include "MachInfoCmdLineOptions.hh"
-#include "OperationPool.hh"
-#include "HWOperation.hh"
-#include "Operation.hh"
 #include "Conversion.hh"
 #include "FUPort.hh"
-
-#include <iostream>
-#include <fstream>
-#include <stdlib.h>
+#include "HWOperation.hh"
+#include "MachInfoCmdLineOptions.hh"
+#include "Machine.hh"
+#include "Operation.hh"
+#include "OperationPool.hh"
 
 static MachInfoCmdLineOptions options;
 
diff --git a/openasip/src/procgen/ProDe/ProDeTextGenerator.cc b/openasip/src/procgen/ProDe/ProDeTextGenerator.cc
index 98f2ecb9cc..24fe0ec769 100644
--- a/openasip/src/procgen/ProDe/ProDeTextGenerator.cc
+++ b/openasip/src/procgen/ProDe/ProDeTextGenerator.cc
@@ -30,10 +30,10 @@
  * @note rating: red
  */
 
-#include <string.h>
-
 #include "ProDeTextGenerator.hh"
 
+#include <cstring>
+
 using std::string;
 
 ProDeTextGenerator* ProDeTextGenerator::instance_ = NULL;
diff --git a/openasip/src/tools/Application.cc b/openasip/src/tools/Application.cc
index 1c5701f7c3..46ad54301c 100644
--- a/openasip/src/tools/Application.cc
+++ b/openasip/src/tools/Application.cc
@@ -43,9 +43,9 @@
 #include <cstdio>
 
 // for backtrace printing:
-#include <signal.h>
-
 #include <sys/types.h>
+
+#include <csignal>
 // macros to evaluate exit status of pclose() (from autoconf manual)
 #ifdef HAVE_SYS_WAIT_H
 # include <sys/wait.h>
diff --git a/openasip/src/tools/PluginTools.icc b/openasip/src/tools/PluginTools.icc
index 3c66ebdfe9..cfa7c8ee88 100644
--- a/openasip/src/tools/PluginTools.icc
+++ b/openasip/src/tools/PluginTools.icc
@@ -31,7 +31,7 @@
  * @note rating: green
  */
 
-#include <stdint.h>
+#include <cstdint>
 
 /**
  * Loads a symbol from a module.
diff --git a/openasip/test/cxxtest/StdioFilePrinter.h b/openasip/test/cxxtest/StdioFilePrinter.h
index d78757b131..32fce0e08f 100644
--- a/openasip/test/cxxtest/StdioFilePrinter.h
+++ b/openasip/test/cxxtest/StdioFilePrinter.h
@@ -32,7 +32,8 @@
 //
 
 #include <cxxtest/ErrorFormatter.h>
-#include <stdio.h>
+
+#include <cstdio>
 
 namespace CxxTest 
 {
diff --git a/openasip/test/cxxtest/X11Gui.h b/openasip/test/cxxtest/X11Gui.h
index 24901a9718..818b835a06 100644
--- a/openasip/test/cxxtest/X11Gui.h
+++ b/openasip/test/cxxtest/X11Gui.h
@@ -35,13 +35,13 @@
 //  -green/-yellow/-red <color> - Sets the colors of the bar
 //
 
-#include <cxxtest/Gui.h>
-
 #include <X11/Xlib.h>
 #include <X11/Xutil.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cxxtest/Gui.h>
+
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
 
 namespace CxxTest
 {
diff --git a/testsuite/systemtest/bintools/Compiler/RegressionTests/data/bool_return_value.cpp b/testsuite/systemtest/bintools/Compiler/RegressionTests/data/bool_return_value.cpp
index 43801e743b..5bab2f6f33 100644
--- a/testsuite/systemtest/bintools/Compiler/RegressionTests/data/bool_return_value.cpp
+++ b/testsuite/systemtest/bintools/Compiler/RegressionTests/data/bool_return_value.cpp
@@ -1,4 +1,4 @@
- #include <stdio.h>
+ #include <cstdio>
 
 volatile int eq = 0;
 volatile int gt = 0;
diff --git a/testsuite/systemtest/procgen/hpu/data/complex.cpp b/testsuite/systemtest/procgen/hpu/data/complex.cpp
index 1b01ea5423..0c3df2ae96 100644
--- a/testsuite/systemtest/procgen/hpu/data/complex.cpp
+++ b/testsuite/systemtest/procgen/hpu/data/complex.cpp
@@ -1,4 +1,4 @@
-#include <stdlib.h>
+#include <cstdlib>
 #include "tceops.h"
 
 #define N 2
diff --git a/testsuite/systemtest/procgen/hpu/data/test_code.cpp b/testsuite/systemtest/procgen/hpu/data/test_code.cpp
index 18dc2fb112..2d08b0b70b 100644
--- a/testsuite/systemtest/procgen/hpu/data/test_code.cpp
+++ b/testsuite/systemtest/procgen/hpu/data/test_code.cpp
@@ -1,4 +1,4 @@
-#include <stdlib.h>
+#include <cstdlib>
 #include "tceops.h"
 
 #define N 2
diff --git a/testsuite/systemtest/procgen/hpu/data/test_code_2.cpp b/testsuite/systemtest/procgen/hpu/data/test_code_2.cpp
index edcb29dad7..78837433bb 100644
--- a/testsuite/systemtest/procgen/hpu/data/test_code_2.cpp
+++ b/testsuite/systemtest/procgen/hpu/data/test_code_2.cpp
@@ -1,4 +1,4 @@
-#include <stdlib.h>
+#include <cstdlib>
 #include "tceops.h"
 
 #define N 2
diff --git a/testsuite/systemtest_long/bintools/PIG/limmTest/data/generate_asm.cc b/testsuite/systemtest_long/bintools/PIG/limmTest/data/generate_asm.cc
index a20e04b6bd..6c8e8180ba 100644
--- a/testsuite/systemtest_long/bintools/PIG/limmTest/data/generate_asm.cc
+++ b/testsuite/systemtest_long/bintools/PIG/limmTest/data/generate_asm.cc
@@ -1,7 +1,7 @@
 #include <cstdlib>
-#include <iostream>
+#include <ctime>
 #include <fstream>
-#include <time.h>
+#include <iostream>
 
 const int TEST_SAMPLES = 1023;
 const std::string TCEASM = "limm_test.tceasm";