diff --git a/examples/cpp/cvrptw.cc b/examples/cpp/cvrptw.cc
index 49b4bbfc2c..73d19ea510 100644
--- a/examples/cpp/cvrptw.cc
+++ b/examples/cpp/cvrptw.cc
@@ -30,7 +30,7 @@
 #include "base/logging.h"
 #include "constraint_solver/routing.h"
 #include "constraint_solver/routing_flags.h"
-#include "cvrptw_lib.h"
+#include "cpp/cvrptw_lib.h"
 
 using operations_research::RoutingModel;
 using operations_research::RoutingSearchParameters;
diff --git a/examples/cpp/cvrptw_lib.cc b/examples/cpp/cvrptw_lib.cc
index e6ac1e33c4..1fc54b103d 100644
--- a/examples/cpp/cvrptw_lib.cc
+++ b/examples/cpp/cvrptw_lib.cc
@@ -11,7 +11,7 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
-#include "cvrptw_lib.h"
+#include "cpp/cvrptw_lib.h"
 
 #include <set>
 
diff --git a/examples/cpp/cvrptw_with_refueling.cc b/examples/cpp/cvrptw_with_refueling.cc
index 5780a3d5c7..de822daefc 100644
--- a/examples/cpp/cvrptw_with_refueling.cc
+++ b/examples/cpp/cvrptw_with_refueling.cc
@@ -28,7 +28,7 @@
 #include "base/logging.h"
 #include "constraint_solver/routing.h"
 #include "constraint_solver/routing_flags.h"
-#include "cvrptw_lib.h"
+#include "cpp/cvrptw_lib.h"
 #include "base/random.h"
 
 using operations_research::GetSeed;
diff --git a/examples/cpp/cvrptw_with_resources.cc b/examples/cpp/cvrptw_with_resources.cc
index 7a3e22a3ed..1e197ead7b 100644
--- a/examples/cpp/cvrptw_with_resources.cc
+++ b/examples/cpp/cvrptw_with_resources.cc
@@ -30,7 +30,7 @@
 #include "base/logging.h"
 #include "constraint_solver/routing.h"
 #include "constraint_solver/routing_flags.h"
-#include "cvrptw_lib.h"
+#include "cpp/cvrptw_lib.h"
 #include "base/random.h"
 
 using operations_research::RoutingModel;
diff --git a/examples/cpp/cvrptw_with_stop_times_and_resources.cc b/examples/cpp/cvrptw_with_stop_times_and_resources.cc
index 0cd983216a..a08fc73069 100644
--- a/examples/cpp/cvrptw_with_stop_times_and_resources.cc
+++ b/examples/cpp/cvrptw_with_stop_times_and_resources.cc
@@ -29,7 +29,7 @@
 #include "base/join.h"
 #include "constraint_solver/routing.h"
 #include "constraint_solver/routing_flags.h"
-#include "cvrptw_lib.h"
+#include "cpp/cvrptw_lib.h"
 #include "base/random.h"
 
 using operations_research::IntervalVar;
diff --git a/examples/cpp/dimacs_assignment.cc b/examples/cpp/dimacs_assignment.cc
index 921d689887..91a308a1a8 100644
--- a/examples/cpp/dimacs_assignment.cc
+++ b/examples/cpp/dimacs_assignment.cc
@@ -25,8 +25,8 @@
 #include "base/stringprintf.h"
 #include "base/timer.h"
 #include "algorithms/hungarian.h"
-#include "parse_dimacs_assignment.h"
-#include "print_dimacs_assignment.h"
+#include "cpp/parse_dimacs_assignment.h"
+#include "cpp/print_dimacs_assignment.h"
 #include "graph/ebert_graph.h"
 #include "graph/linear_assignment.h"
 
diff --git a/examples/cpp/fap_model_printer.cc b/examples/cpp/fap_model_printer.cc
index 4ac6816987..0be1c4bd3a 100644
--- a/examples/cpp/fap_model_printer.cc
+++ b/examples/cpp/fap_model_printer.cc
@@ -12,7 +12,7 @@
 // limitations under the License.
 //
 
-#include "fap_model_printer.h"
+#include "cpp/fap_model_printer.h"
 
 #include <map>
 #include <string>
diff --git a/examples/cpp/fap_model_printer.h b/examples/cpp/fap_model_printer.h
index 5c301abc57..877d8aec51 100644
--- a/examples/cpp/fap_model_printer.h
+++ b/examples/cpp/fap_model_printer.h
@@ -21,7 +21,7 @@
 #include <map>
 #include <vector>
 
-#include "fap_parser.h"
+#include "cpp/fap_parser.h"
 
 using std::string;
 
diff --git a/examples/cpp/fap_parser.cc b/examples/cpp/fap_parser.cc
index 0504df5eb0..341668d583 100644
--- a/examples/cpp/fap_parser.cc
+++ b/examples/cpp/fap_parser.cc
@@ -20,7 +20,7 @@
 #include "base/concise_iterator.h"
 #include "base/map_util.h"
 
-#include "fap_parser.h"
+#include "cpp/fap_parser.h"
 
 namespace operations_research {
 
diff --git a/examples/cpp/fap_utilities.cc b/examples/cpp/fap_utilities.cc
index f89be70e16..60d2dc17ec 100644
--- a/examples/cpp/fap_utilities.cc
+++ b/examples/cpp/fap_utilities.cc
@@ -12,7 +12,7 @@
 // limitations under the License.
 //
 
-#include "fap_utilities.h"
+#include "cpp/fap_utilities.h"
 
 #include <map>
 #include <set>
diff --git a/examples/cpp/flexible_jobshop.cc b/examples/cpp/flexible_jobshop.cc
index 17a7c6c08f..03cfb60d7f 100644
--- a/examples/cpp/flexible_jobshop.cc
+++ b/examples/cpp/flexible_jobshop.cc
@@ -41,7 +41,7 @@
 #include "base/logging.h"
 #include "base/stringprintf.h"
 #include "constraint_solver/constraint_solver.h"
-#include "flexible_jobshop.h"
+#include "cpp/flexible_jobshop.h"
 #include "util/string_array.h"
 
 DEFINE_string(
diff --git a/examples/cpp/frequency_assignment_problem.cc b/examples/cpp/frequency_assignment_problem.cc
index 678508c0eb..90e095117d 100644
--- a/examples/cpp/frequency_assignment_problem.cc
+++ b/examples/cpp/frequency_assignment_problem.cc
@@ -51,9 +51,9 @@
 #include "base/map_util.h"
 #include "base/hash.h"
 #include "constraint_solver/constraint_solver.h"
-#include "fap_model_printer.h"
-#include "fap_parser.h"
-#include "fap_utilities.h"
+#include "cpp/fap_model_printer.h"
+#include "cpp/fap_parser.h"
+#include "cpp/fap_utilities.h"
 
 DEFINE_string(directory, "", "Specifies the directory of the data.");
 DEFINE_string(evaluator, "",
diff --git a/examples/cpp/jobshop.cc b/examples/cpp/jobshop.cc
index c3d845b26f..7b8ea82cb0 100644
--- a/examples/cpp/jobshop.cc
+++ b/examples/cpp/jobshop.cc
@@ -33,7 +33,7 @@
 //
 // Search will then be applied on the sequence constraints.
 
-#include "jobshop.h"
+#include "cpp/jobshop.h"
 #include <cstdio>
 #include <cstdlib>
 
diff --git a/examples/cpp/jobshop_earlytardy.cc b/examples/cpp/jobshop_earlytardy.cc
index bcede9a784..2e05957e2a 100644
--- a/examples/cpp/jobshop_earlytardy.cc
+++ b/examples/cpp/jobshop_earlytardy.cc
@@ -44,8 +44,8 @@
 #include "constraint_solver/constraint_solver.h"
 #include "linear_solver/linear_solver.h"
 #include "util/string_array.h"
-#include "jobshop_earlytardy.h"
-#include "jobshop_ls.h"
+#include "cpp/jobshop_earlytardy.h"
+#include "cpp/jobshop_ls.h"
 
 DEFINE_string(
     jet_file,
diff --git a/examples/cpp/jobshop_ls.cc b/examples/cpp/jobshop_ls.cc
index d4deaa0a5c..d6b941e9c5 100644
--- a/examples/cpp/jobshop_ls.cc
+++ b/examples/cpp/jobshop_ls.cc
@@ -33,7 +33,7 @@
 //
 // Search will be implemented as local search on the sequence variables.
 
-#include "jobshop_ls.h"
+#include "cpp/jobshop_ls.h"
 #include <cstdio>
 #include <cstdlib>
 
@@ -45,7 +45,7 @@
 #include "base/bitmap.h"
 #include "constraint_solver/constraint_solver.h"
 #include "constraint_solver/constraint_solveri.h"
-#include "jobshop.h"
+#include "cpp/jobshop.h"
 
 DEFINE_string(
     data_file, "",
diff --git a/examples/cpp/parse_dimacs_assignment.cc b/examples/cpp/parse_dimacs_assignment.cc
index 98f16aeef0..9d0d9f00d7 100644
--- a/examples/cpp/parse_dimacs_assignment.cc
+++ b/examples/cpp/parse_dimacs_assignment.cc
@@ -12,7 +12,7 @@
 // limitations under the License.
 
 
-#include "parse_dimacs_assignment.h"
+#include "cpp/parse_dimacs_assignment.h"
 
 #include "base/commandlineflags.h"
 
diff --git a/examples/cpp/print_dimacs_assignment.cc b/examples/cpp/print_dimacs_assignment.cc
index f6aebbb486..4098821e38 100644
--- a/examples/cpp/print_dimacs_assignment.cc
+++ b/examples/cpp/print_dimacs_assignment.cc
@@ -11,7 +11,7 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
-#include "print_dimacs_assignment.h"
+#include "cpp/print_dimacs_assignment.h"
 
 #include <cstdio>
 #include <string>
diff --git a/examples/cpp/sat_runner.cc b/examples/cpp/sat_runner.cc
index 8d153c5561..3fbc8f73f4 100644
--- a/examples/cpp/sat_runner.cc
+++ b/examples/cpp/sat_runner.cc
@@ -27,9 +27,9 @@
 #include "base/strutil.h"
 #include "algorithms/sparse_permutation.h"
 #include "sat/boolean_problem.h"
-#include "opb_reader.h"
+#include "cpp/opb_reader.h"
 #include "sat/optimization.h"
-#include "sat_cnf_reader.h"
+#include "cpp/sat_cnf_reader.h"
 #include "sat/sat_solver.h"
 #include "sat/simplification.h"
 #include "sat/symmetry.h"
diff --git a/makefiles/Makefile.unix b/makefiles/Makefile.unix
index 962fb3378a..933d42388e 100644
--- a/makefiles/Makefile.unix
+++ b/makefiles/Makefile.unix
@@ -265,11 +265,11 @@ ifeq ($(PLATFORM),MACOSX)
   FLEX = dependencies/install/bin/flex
 endif  # MAC OS X
 
-CFLAGS = $(DEBUG) -I$(INC_DIR) -I$(EX_DIR)/cpp -I$(GEN_DIR) $(GFLAGS_INC) $(ARCH) \
+CFLAGS = $(DEBUG) -I$(INC_DIR) -I$(EX_DIR) -I$(GEN_DIR) $(GFLAGS_INC) $(ARCH) \
 	-Wno-deprecated $(PROTOBUF_INC) $(CBC_INC) $(CLP_INC) $(GLPK_INC) \
         $(SCIP_INC) $(SLM_INC) $(GUROBI_INC) $(CPLEX_INC) -DUSE_GLOP -DUSE_BOP $(SPARSEHASH_INC)
 
-JNIFLAGS = $(JNIDEBUG) -I$(INC_DIR) -I$(EX_DIR)/cpp -I$(GEN_DIR) $(GFLAGS_INC) $(ARCH) \
+JNIFLAGS = $(JNIDEBUG) -I$(INC_DIR) -I$(EX_DIR) -I$(GEN_DIR) $(GFLAGS_INC) $(ARCH) \
         -Wno-deprecated $(PROTOBUF_INC) $(CBC_INC) $(CLP_INC) $(GLPK_INC) $(SCIP_INC) $(SLM_INC) $(GUROBI_INC) $(CPLEX_INC) -DUSE_GLOP -DUSE_BOP
 DYNAMIC_LD_FLAGS = $(DYNAMIC_GFLAGS_LNK) $(ZLIB_LNK) $(DYNAMIC_PROTOBUF_LNK) $(SYS_LNK)
 DYNAMIC_LD_LP_DEPS = $(DYNAMIC_GLPK_LNK) $(DYNAMIC_CBC_LNK) $(DYNAMIC_CLP_LNK) $(DYNAMIC_SLM_LNK) $(DYNAMIC_GUROBI_LNK) $(DYNAMIC_CPLEX_LNK)
diff --git a/makefiles/Makefile.win b/makefiles/Makefile.win
index fd14326556..e0fe36dea7 100644
--- a/makefiles/Makefile.win
+++ b/makefiles/Makefile.win
@@ -117,7 +117,7 @@ JAVAC_BIN="$(WINDOWS_JDK_DIR)/bin/javac"
 JAVA_BIN="$(WINDOWS_JDK_DIR)/bin/java"
 JAR_BIN="$(WINDOWS_JDK_DIR)/bin/jar"
 
-CFLAGS= -nologo $(SYSCFLAGS) $(DEBUG) /I$(INC_DIR) /I$(EX_DIR)\\cpp /I$(GEN_DIR) \
+CFLAGS= -nologo $(SYSCFLAGS) $(DEBUG) /I$(INC_DIR) /I$(EX_DIR) /I$(GEN_DIR) \
         $(GFLAGS_INC) $(ZLIB_INC) $(MINISAT_INC) $(PROTOBUF_INC) $(CBC_INC) \
         $(CLP_INC) $(GLPK_INC) $(SCIP_INC) $(SLM_INC) $(GUROBI_INC) /DUSE_GLOP /DUSE_BOP \
         /D__WIN32__  $(SPARSEHASH_INC) /DPSAPI_VERSION=1