diff --git a/include/BlockTriangular.hh b/BlockTriangular.hh
similarity index 100%
rename from include/BlockTriangular.hh
rename to BlockTriangular.hh
diff --git a/include/CodeInterpreter.hh b/CodeInterpreter.hh
similarity index 100%
rename from include/CodeInterpreter.hh
rename to CodeInterpreter.hh
diff --git a/include/ComputingTasks.hh b/ComputingTasks.hh
similarity index 100%
rename from include/ComputingTasks.hh
rename to ComputingTasks.hh
diff --git a/include/DataTree.hh b/DataTree.hh
similarity index 100%
rename from include/DataTree.hh
rename to DataTree.hh
diff --git a/include/ExprNode.hh b/ExprNode.hh
similarity index 100%
rename from include/ExprNode.hh
rename to ExprNode.hh
diff --git a/include/IncidenceMatrix.hh b/IncidenceMatrix.hh
similarity index 100%
rename from include/IncidenceMatrix.hh
rename to IncidenceMatrix.hh
diff --git a/Makefile b/Makefile
index 7b4477c91beecc23b401d400237a193c02f8c409..501bdf9e63196707c1a04de84c32171517003e45 100644
--- a/Makefile
+++ b/Makefile
@@ -65,8 +65,6 @@ MACRO_OBJS = \
 	macro/MacroDriver.o \
 	macro/MacroValue.o
 
-$(MAIN_OBJS) $(MAIN_OBJS:.o=.d): CPPFLAGS = -Iinclude
-
 
 # Build rules
 
@@ -83,9 +81,8 @@ $(DYNARE_M): $(MAIN_OBJS) $(MACRO_OBJS)
 DynareFlex.cc: DynareFlex.ll
 	flex -oDynareFlex.cc DynareFlex.ll
 
-DynareBison.cc include/DynareBison.hh include/location.hh include/stack.hh include/position.hh: DynareBison.yy
+DynareBison.cc DynareBison.hh location.hh stack.hh position.hh: DynareBison.yy
 	bison --verbose -o DynareBison.cc DynareBison.yy
-	mv DynareBison.hh location.hh stack.hh position.hh include/
 
 macro/MacroFlex.cc: macro/MacroFlex.ll
 	cd macro && flex -oMacroFlex.cc MacroFlex.ll
@@ -105,8 +102,7 @@ macro/MacroBison.cc macro/MacroBison.hh macro/location.hh macro/stack.hh macro/p
 	 sed 's,\($*\)\.o[ :]*,\1.o $@ : ,g' < $@.$$$$ > $@; \
 	 rm -f $@.$$$$
 
-# These files are included in the .d files without their path, so we force them
-vpath DynareBison.hh include
+# As DynareBison.hh, this file is included in the .d files without its path (since it is generated), so we force the path
 vpath MacroBison.hh macro
 
 -include $(MAIN_OBJS:.o=.d)
@@ -117,15 +113,14 @@ vpath MacroBison.hh macro
 
 .PHONY: clean
 clean:
-	rm -f *.o *.d \
-		*~ include/*~ \
+	rm -f *.o *.d *~ \
 		DynareFlex.cc \
 		DynareBison.output \
 		DynareBison.cc \
-		include/position.hh \
-		include/stack.hh \
-		include/location.hh \
-		include/DynareBison.hh \
+		position.hh \
+		stack.hh \
+		location.hh \
+		DynareBison.hh \
 		$(DYNARE_M)
 	cd macro && rm -f *.o *.d *~ \
 		MacroFlex.cc \
diff --git a/include/MatlabFile.hh b/MatlabFile.hh
similarity index 100%
rename from include/MatlabFile.hh
rename to MatlabFile.hh
diff --git a/include/ModFile.hh b/ModFile.hh
similarity index 100%
rename from include/ModFile.hh
rename to ModFile.hh
diff --git a/include/ModelBlocks.hh b/ModelBlocks.hh
similarity index 100%
rename from include/ModelBlocks.hh
rename to ModelBlocks.hh
diff --git a/include/ModelNormalization.hh b/ModelNormalization.hh
similarity index 100%
rename from include/ModelNormalization.hh
rename to ModelNormalization.hh
diff --git a/include/ModelTree.hh b/ModelTree.hh
similarity index 100%
rename from include/ModelTree.hh
rename to ModelTree.hh
diff --git a/include/Model_Graph.hh b/Model_Graph.hh
similarity index 100%
rename from include/Model_Graph.hh
rename to Model_Graph.hh
diff --git a/include/NumericalConstants.hh b/NumericalConstants.hh
similarity index 100%
rename from include/NumericalConstants.hh
rename to NumericalConstants.hh
diff --git a/include/NumericalInitialization.hh b/NumericalInitialization.hh
similarity index 100%
rename from include/NumericalInitialization.hh
rename to NumericalInitialization.hh
diff --git a/include/ParsingDriver.hh b/ParsingDriver.hh
similarity index 100%
rename from include/ParsingDriver.hh
rename to ParsingDriver.hh
diff --git a/include/Shocks.hh b/Shocks.hh
similarity index 100%
rename from include/Shocks.hh
rename to Shocks.hh
diff --git a/include/SigmaeInitialization.hh b/SigmaeInitialization.hh
similarity index 100%
rename from include/SigmaeInitialization.hh
rename to SigmaeInitialization.hh
diff --git a/include/Statement.hh b/Statement.hh
similarity index 100%
rename from include/Statement.hh
rename to Statement.hh
diff --git a/include/SymbolList.hh b/SymbolList.hh
similarity index 100%
rename from include/SymbolList.hh
rename to SymbolList.hh
diff --git a/include/SymbolTable.hh b/SymbolTable.hh
similarity index 100%
rename from include/SymbolTable.hh
rename to SymbolTable.hh
diff --git a/include/VariableTable.hh b/VariableTable.hh
similarity index 100%
rename from include/VariableTable.hh
rename to VariableTable.hh