diff --git a/cartographer/io/hybrid_grid_points_processor.h b/cartographer/io/hybrid_grid_points_processor.h
index 1d80655..0b598b9 100644
--- a/cartographer/io/hybrid_grid_points_processor.h
+++ b/cartographer/io/hybrid_grid_points_processor.h
@@ -10,8 +10,8 @@
 #include "cartographer/io/points_batch.h"
 #include "cartographer/io/points_processor.h"
 #include "cartographer/mapping/3d/hybrid_grid.h"
-#include "cartographer/mapping/3d/proto/range_data_inserter_options_3d.pb.h"
 #include "cartographer/mapping/3d/range_data_inserter_3d.h"
+#include "cartographer/mapping/proto/3d/range_data_inserter_options_3d.pb.h"
 
 namespace cartographer {
 namespace io {
diff --git a/cartographer/io/probability_grid_points_processor.h b/cartographer/io/probability_grid_points_processor.h
index 4d94736..5278e29 100644
--- a/cartographer/io/probability_grid_points_processor.h
+++ b/cartographer/io/probability_grid_points_processor.h
@@ -25,7 +25,7 @@
 #include "cartographer/io/points_processor.h"
 #include "cartographer/mapping/2d/probability_grid.h"
 #include "cartographer/mapping/2d/probability_grid_range_data_inserter_2d.h"
-#include "cartographer/mapping/2d/proto/probability_grid_range_data_inserter_options_2d.pb.h"
+#include "cartographer/mapping/proto/2d/probability_grid_range_data_inserter_options_2d.pb.h"
 #include "cartographer/mapping/proto/trajectory.pb.h"
 
 namespace cartographer {
diff --git a/cartographer/mapping/2d/grid_2d.h b/cartographer/mapping/2d/grid_2d.h
index 1f8c590..72bbc63 100644
--- a/cartographer/mapping/2d/grid_2d.h
+++ b/cartographer/mapping/2d/grid_2d.h
@@ -20,9 +20,9 @@
 #include <vector>
 
 #include "cartographer/mapping/2d/map_limits.h"
-#include "cartographer/mapping/2d/proto/grid_2d.pb.h"
-#include "cartographer/mapping/2d/proto/submaps_options_2d.pb.h"
 #include "cartographer/mapping/grid_interface.h"
+#include "cartographer/mapping/proto/2d/grid_2d.pb.h"
+#include "cartographer/mapping/proto/2d/submaps_options_2d.pb.h"
 #include "cartographer/mapping/proto/submap_visualization.pb.h"
 
 namespace cartographer {
diff --git a/cartographer/mapping/2d/map_limits.h b/cartographer/mapping/2d/map_limits.h
index d131bcb..3d731b9 100644
--- a/cartographer/mapping/2d/map_limits.h
+++ b/cartographer/mapping/2d/map_limits.h
@@ -23,8 +23,8 @@
 #include "Eigen/Core"
 #include "Eigen/Geometry"
 #include "cartographer/common/math.h"
-#include "cartographer/mapping/2d/proto/map_limits.pb.h"
 #include "cartographer/mapping/2d/xy_index.h"
+#include "cartographer/mapping/proto/2d/map_limits.pb.h"
 #include "cartographer/mapping/trajectory_node.h"
 #include "cartographer/sensor/point_cloud.h"
 #include "cartographer/sensor/range_data.h"
diff --git a/cartographer/mapping/2d/probability_grid_range_data_inserter_2d.h b/cartographer/mapping/2d/probability_grid_range_data_inserter_2d.h
index 756ce1c..83a04b8 100644
--- a/cartographer/mapping/2d/probability_grid_range_data_inserter_2d.h
+++ b/cartographer/mapping/2d/probability_grid_range_data_inserter_2d.h
@@ -23,8 +23,8 @@
 #include "cartographer/common/lua_parameter_dictionary.h"
 #include "cartographer/common/port.h"
 #include "cartographer/mapping/2d/probability_grid.h"
-#include "cartographer/mapping/2d/proto/probability_grid_range_data_inserter_options_2d.pb.h"
 #include "cartographer/mapping/2d/xy_index.h"
+#include "cartographer/mapping/proto/2d/probability_grid_range_data_inserter_options_2d.pb.h"
 #include "cartographer/mapping/range_data_inserter_interface.h"
 #include "cartographer/sensor/point_cloud.h"
 #include "cartographer/sensor/range_data.h"
diff --git a/cartographer/mapping/2d/submap_2d.h b/cartographer/mapping/2d/submap_2d.h
index 5e3e807..8a58de3 100644
--- a/cartographer/mapping/2d/submap_2d.h
+++ b/cartographer/mapping/2d/submap_2d.h
@@ -24,7 +24,7 @@
 #include "cartographer/common/lua_parameter_dictionary.h"
 #include "cartographer/mapping/2d/grid_2d.h"
 #include "cartographer/mapping/2d/map_limits.h"
-#include "cartographer/mapping/2d/proto/submaps_options_2d.pb.h"
+#include "cartographer/mapping/proto/2d/submaps_options_2d.pb.h"
 #include "cartographer/mapping/proto/serialization.pb.h"
 #include "cartographer/mapping/proto/submap_visualization.pb.h"
 #include "cartographer/mapping/range_data_inserter_interface.h"
diff --git a/cartographer/mapping/2d/xy_index.h b/cartographer/mapping/2d/xy_index.h
index 1d0e78b..64acf27 100644
--- a/cartographer/mapping/2d/xy_index.h
+++ b/cartographer/mapping/2d/xy_index.h
@@ -25,7 +25,7 @@
 #include "Eigen/Core"
 #include "cartographer/common/math.h"
 #include "cartographer/common/port.h"
-#include "cartographer/mapping/2d/proto/cell_limits.pb.h"
+#include "cartographer/mapping/proto/2d/cell_limits.pb.h"
 #include "glog/logging.h"
 
 namespace cartographer {
diff --git a/cartographer/mapping/3d/hybrid_grid.h b/cartographer/mapping/3d/hybrid_grid.h
index 23bd7bd..423f9c9 100644
--- a/cartographer/mapping/3d/hybrid_grid.h
+++ b/cartographer/mapping/3d/hybrid_grid.h
@@ -27,8 +27,8 @@
 #include "cartographer/common/make_unique.h"
 #include "cartographer/common/math.h"
 #include "cartographer/common/port.h"
-#include "cartographer/mapping/3d/proto/hybrid_grid.pb.h"
 #include "cartographer/mapping/probability_values.h"
+#include "cartographer/mapping/proto/3d/hybrid_grid.pb.h"
 #include "cartographer/transform/transform.h"
 #include "glog/logging.h"
 
diff --git a/cartographer/mapping/3d/range_data_inserter_3d.h b/cartographer/mapping/3d/range_data_inserter_3d.h
index 524dbfa..b6b0bcd 100644
--- a/cartographer/mapping/3d/range_data_inserter_3d.h
+++ b/cartographer/mapping/3d/range_data_inserter_3d.h
@@ -18,7 +18,7 @@
 #define CARTOGRAPHER_MAPPING_3D_RANGE_DATA_INSERTER_3D_H_
 
 #include "cartographer/mapping/3d/hybrid_grid.h"
-#include "cartographer/mapping/3d/proto/range_data_inserter_options_3d.pb.h"
+#include "cartographer/mapping/proto/3d/range_data_inserter_options_3d.pb.h"
 #include "cartographer/sensor/point_cloud.h"
 #include "cartographer/sensor/range_data.h"
 
diff --git a/cartographer/mapping/3d/submap_3d.h b/cartographer/mapping/3d/submap_3d.h
index 5a1367f..9fc6e0f 100644
--- a/cartographer/mapping/3d/submap_3d.h
+++ b/cartographer/mapping/3d/submap_3d.h
@@ -24,9 +24,9 @@
 #include "Eigen/Geometry"
 #include "cartographer/common/port.h"
 #include "cartographer/mapping/3d/hybrid_grid.h"
-#include "cartographer/mapping/3d/proto/submaps_options_3d.pb.h"
 #include "cartographer/mapping/3d/range_data_inserter_3d.h"
 #include "cartographer/mapping/id.h"
+#include "cartographer/mapping/proto/3d/submaps_options_3d.pb.h"
 #include "cartographer/mapping/proto/serialization.pb.h"
 #include "cartographer/mapping/proto/submap_visualization.pb.h"
 #include "cartographer/mapping/submaps.h"
diff --git a/cartographer/mapping/internal/2d/local_trajectory_builder_2d.h b/cartographer/mapping/internal/2d/local_trajectory_builder_2d.h
index 77de6db..bfc47b3 100644
--- a/cartographer/mapping/internal/2d/local_trajectory_builder_2d.h
+++ b/cartographer/mapping/internal/2d/local_trajectory_builder_2d.h
@@ -21,13 +21,13 @@
 #include <memory>
 
 #include "cartographer/common/time.h"
-#include "cartographer/mapping/2d/proto/local_trajectory_builder_options_2d.pb.h"
 #include "cartographer/mapping/2d/submap_2d.h"
 #include "cartographer/mapping/internal/2d/scan_matching/ceres_scan_matcher_2d.h"
 #include "cartographer/mapping/internal/2d/scan_matching/real_time_correlative_scan_matcher_2d.h"
 #include "cartographer/mapping/internal/motion_filter.h"
 #include "cartographer/mapping/internal/range_data_collator.h"
 #include "cartographer/mapping/pose_extrapolator.h"
+#include "cartographer/mapping/proto/2d/local_trajectory_builder_options_2d.pb.h"
 #include "cartographer/metrics/family_factory.h"
 #include "cartographer/sensor/imu_data.h"
 #include "cartographer/sensor/internal/voxel_filter.h"
diff --git a/cartographer/mapping/internal/2d/local_trajectory_builder_options_2d.h b/cartographer/mapping/internal/2d/local_trajectory_builder_options_2d.h
index 4b52e65..32fa742 100644
--- a/cartographer/mapping/internal/2d/local_trajectory_builder_options_2d.h
+++ b/cartographer/mapping/internal/2d/local_trajectory_builder_options_2d.h
@@ -18,7 +18,7 @@
 #define CARTOGRAPHER_MAPPING_INTERNAL_2D_LOCAL_TRAJECTORY_BUILDER_OPTIONS_2D_H_
 
 #include "cartographer/common/lua_parameter_dictionary.h"
-#include "cartographer/mapping/2d/proto/local_trajectory_builder_options_2d.pb.h"
+#include "cartographer/mapping/proto/2d/local_trajectory_builder_options_2d.pb.h"
 
 namespace cartographer {
 namespace mapping {
diff --git a/cartographer/mapping/internal/2d/pose_graph_2d.cc b/cartographer/mapping/internal/2d/pose_graph_2d.cc
index 8764a7c..73d21bd 100644
--- a/cartographer/mapping/internal/2d/pose_graph_2d.cc
+++ b/cartographer/mapping/internal/2d/pose_graph_2d.cc
@@ -31,7 +31,7 @@
 #include "Eigen/Eigenvalues"
 #include "cartographer/common/make_unique.h"
 #include "cartographer/common/math.h"
-#include "cartographer/mapping/pose_graph/proto/constraint_builder_options.pb.h"
+#include "cartographer/mapping/proto/pose_graph/constraint_builder_options.pb.h"
 #include "cartographer/sensor/compressed_point_cloud.h"
 #include "cartographer/sensor/internal/voxel_filter.h"
 #include "glog/logging.h"
diff --git a/cartographer/mapping/internal/2d/scan_matching/ceres_scan_matcher_2d.h b/cartographer/mapping/internal/2d/scan_matching/ceres_scan_matcher_2d.h
index fcd83e6..48108d5 100644
--- a/cartographer/mapping/internal/2d/scan_matching/ceres_scan_matcher_2d.h
+++ b/cartographer/mapping/internal/2d/scan_matching/ceres_scan_matcher_2d.h
@@ -23,7 +23,7 @@
 #include "Eigen/Core"
 #include "cartographer/common/lua_parameter_dictionary.h"
 #include "cartographer/mapping/2d/grid_2d.h"
-#include "cartographer/mapping/2d/scan_matching/proto/ceres_scan_matcher_options_2d.pb.h"
+#include "cartographer/mapping/proto/scan_matching/ceres_scan_matcher_options_2d.pb.h"
 #include "cartographer/sensor/point_cloud.h"
 #include "ceres/ceres.h"
 
diff --git a/cartographer/mapping/internal/2d/scan_matching/fast_correlative_scan_matcher_2d.h b/cartographer/mapping/internal/2d/scan_matching/fast_correlative_scan_matcher_2d.h
index d6fb855..6498307 100644
--- a/cartographer/mapping/internal/2d/scan_matching/fast_correlative_scan_matcher_2d.h
+++ b/cartographer/mapping/internal/2d/scan_matching/fast_correlative_scan_matcher_2d.h
@@ -31,8 +31,8 @@
 #include "Eigen/Core"
 #include "cartographer/common/port.h"
 #include "cartographer/mapping/2d/grid_2d.h"
-#include "cartographer/mapping/2d/scan_matching/proto/fast_correlative_scan_matcher_options_2d.pb.h"
 #include "cartographer/mapping/internal/2d/scan_matching/correlative_scan_matcher_2d.h"
+#include "cartographer/mapping/proto/scan_matching/fast_correlative_scan_matcher_options_2d.pb.h"
 #include "cartographer/sensor/point_cloud.h"
 
 namespace cartographer {
diff --git a/cartographer/mapping/internal/2d/scan_matching/real_time_correlative_scan_matcher_2d.h b/cartographer/mapping/internal/2d/scan_matching/real_time_correlative_scan_matcher_2d.h
index a991d27..ab68471 100644
--- a/cartographer/mapping/internal/2d/scan_matching/real_time_correlative_scan_matcher_2d.h
+++ b/cartographer/mapping/internal/2d/scan_matching/real_time_correlative_scan_matcher_2d.h
@@ -43,7 +43,7 @@
 #include "Eigen/Core"
 #include "cartographer/mapping/2d/probability_grid.h"
 #include "cartographer/mapping/internal/2d/scan_matching/correlative_scan_matcher_2d.h"
-#include "cartographer/mapping/scan_matching/proto/real_time_correlative_scan_matcher_options.pb.h"
+#include "cartographer/mapping/proto/scan_matching/real_time_correlative_scan_matcher_options.pb.h"
 
 namespace cartographer {
 namespace mapping {
diff --git a/cartographer/mapping/internal/3d/local_trajectory_builder_3d.cc b/cartographer/mapping/internal/3d/local_trajectory_builder_3d.cc
index bb66fa0..d332663 100644
--- a/cartographer/mapping/internal/3d/local_trajectory_builder_3d.cc
+++ b/cartographer/mapping/internal/3d/local_trajectory_builder_3d.cc
@@ -20,11 +20,11 @@
 
 #include "cartographer/common/make_unique.h"
 #include "cartographer/common/time.h"
-#include "cartographer/mapping/3d/proto/local_trajectory_builder_options_3d.pb.h"
-#include "cartographer/mapping/3d/proto/submaps_options_3d.pb.h"
-#include "cartographer/mapping/3d/scan_matching/proto/ceres_scan_matcher_options_3d.pb.h"
 #include "cartographer/mapping/internal/3d/scan_matching/rotational_scan_matcher.h"
-#include "cartographer/mapping/scan_matching/proto/real_time_correlative_scan_matcher_options.pb.h"
+#include "cartographer/mapping/proto/3d/local_trajectory_builder_options_3d.pb.h"
+#include "cartographer/mapping/proto/3d/submaps_options_3d.pb.h"
+#include "cartographer/mapping/proto/scan_matching//ceres_scan_matcher_options_3d.pb.h"
+#include "cartographer/mapping/proto/scan_matching//real_time_correlative_scan_matcher_options.pb.h"
 #include "glog/logging.h"
 
 namespace cartographer {
diff --git a/cartographer/mapping/internal/3d/local_trajectory_builder_3d.h b/cartographer/mapping/internal/3d/local_trajectory_builder_3d.h
index 99ca19c..02fdeef 100644
--- a/cartographer/mapping/internal/3d/local_trajectory_builder_3d.h
+++ b/cartographer/mapping/internal/3d/local_trajectory_builder_3d.h
@@ -21,13 +21,13 @@
 #include <memory>
 
 #include "cartographer/common/time.h"
-#include "cartographer/mapping/3d/proto/local_trajectory_builder_options_3d.pb.h"
 #include "cartographer/mapping/3d/submap_3d.h"
 #include "cartographer/mapping/internal/3d/scan_matching/ceres_scan_matcher_3d.h"
 #include "cartographer/mapping/internal/3d/scan_matching/real_time_correlative_scan_matcher_3d.h"
 #include "cartographer/mapping/internal/motion_filter.h"
 #include "cartographer/mapping/internal/range_data_collator.h"
 #include "cartographer/mapping/pose_extrapolator.h"
+#include "cartographer/mapping/proto/3d/local_trajectory_builder_options_3d.pb.h"
 #include "cartographer/metrics/family_factory.h"
 #include "cartographer/sensor/imu_data.h"
 #include "cartographer/sensor/internal/voxel_filter.h"
diff --git a/cartographer/mapping/internal/3d/local_trajectory_builder_options_3d.h b/cartographer/mapping/internal/3d/local_trajectory_builder_options_3d.h
index 5a0241b..b01b298 100644
--- a/cartographer/mapping/internal/3d/local_trajectory_builder_options_3d.h
+++ b/cartographer/mapping/internal/3d/local_trajectory_builder_options_3d.h
@@ -18,7 +18,7 @@
 #define CARTOGRAPHER_MAPPING_INTERNAL_3D_LOCAL_TRAJECTORY_BUILDER_OPTIONS_3D_H_
 
 #include "cartographer/common/lua_parameter_dictionary.h"
-#include "cartographer/mapping/3d/proto/local_trajectory_builder_options_3d.pb.h"
+#include "cartographer/mapping/proto/3d/local_trajectory_builder_options_3d.pb.h"
 
 namespace cartographer {
 namespace mapping {
diff --git a/cartographer/mapping/internal/3d/pose_graph_3d.cc b/cartographer/mapping/internal/3d/pose_graph_3d.cc
index 07eab26..032e0c6 100644
--- a/cartographer/mapping/internal/3d/pose_graph_3d.cc
+++ b/cartographer/mapping/internal/3d/pose_graph_3d.cc
@@ -30,7 +30,7 @@
 #include "Eigen/Eigenvalues"
 #include "cartographer/common/make_unique.h"
 #include "cartographer/common/math.h"
-#include "cartographer/mapping/pose_graph/proto/constraint_builder_options.pb.h"
+#include "cartographer/mapping/proto/pose_graph/constraint_builder_options.pb.h"
 #include "cartographer/sensor/compressed_point_cloud.h"
 #include "cartographer/sensor/internal/voxel_filter.h"
 #include "cartographer/transform/transform.h"
diff --git a/cartographer/mapping/internal/3d/scan_matching/ceres_scan_matcher_3d.h b/cartographer/mapping/internal/3d/scan_matching/ceres_scan_matcher_3d.h
index 9e064b0..ffbaa0c 100644
--- a/cartographer/mapping/internal/3d/scan_matching/ceres_scan_matcher_3d.h
+++ b/cartographer/mapping/internal/3d/scan_matching/ceres_scan_matcher_3d.h
@@ -23,7 +23,7 @@
 #include "Eigen/Core"
 #include "cartographer/common/lua_parameter_dictionary.h"
 #include "cartographer/mapping/3d/hybrid_grid.h"
-#include "cartographer/mapping/3d/scan_matching/proto/ceres_scan_matcher_options_3d.pb.h"
+#include "cartographer/mapping/proto/scan_matching/ceres_scan_matcher_options_3d.pb.h"
 #include "cartographer/sensor/point_cloud.h"
 #include "cartographer/transform/rigid_transform.h"
 
diff --git a/cartographer/mapping/internal/3d/scan_matching/fast_correlative_scan_matcher_3d.cc b/cartographer/mapping/internal/3d/scan_matching/fast_correlative_scan_matcher_3d.cc
index 9b8c7bf..66e4fbe 100644
--- a/cartographer/mapping/internal/3d/scan_matching/fast_correlative_scan_matcher_3d.cc
+++ b/cartographer/mapping/internal/3d/scan_matching/fast_correlative_scan_matcher_3d.cc
@@ -24,8 +24,8 @@
 #include "Eigen/Geometry"
 #include "cartographer/common/make_unique.h"
 #include "cartographer/common/math.h"
-#include "cartographer/mapping/3d/scan_matching/proto/fast_correlative_scan_matcher_options_3d.pb.h"
 #include "cartographer/mapping/internal/3d/scan_matching/low_resolution_matcher.h"
+#include "cartographer/mapping/proto/scan_matching//fast_correlative_scan_matcher_options_3d.pb.h"
 #include "cartographer/transform/transform.h"
 #include "glog/logging.h"
 
diff --git a/cartographer/mapping/internal/3d/scan_matching/fast_correlative_scan_matcher_3d.h b/cartographer/mapping/internal/3d/scan_matching/fast_correlative_scan_matcher_3d.h
index 5033776..292ff06 100644
--- a/cartographer/mapping/internal/3d/scan_matching/fast_correlative_scan_matcher_3d.h
+++ b/cartographer/mapping/internal/3d/scan_matching/fast_correlative_scan_matcher_3d.h
@@ -26,10 +26,10 @@
 #include "Eigen/Core"
 #include "cartographer/common/port.h"
 #include "cartographer/mapping/3d/hybrid_grid.h"
-#include "cartographer/mapping/3d/scan_matching/proto/fast_correlative_scan_matcher_options_3d.pb.h"
 #include "cartographer/mapping/internal/2d/scan_matching/fast_correlative_scan_matcher_2d.h"
 #include "cartographer/mapping/internal/3d/scan_matching/precomputation_grid_3d.h"
 #include "cartographer/mapping/internal/3d/scan_matching/rotational_scan_matcher.h"
+#include "cartographer/mapping/proto/scan_matching/fast_correlative_scan_matcher_options_3d.pb.h"
 #include "cartographer/mapping/trajectory_node.h"
 #include "cartographer/sensor/point_cloud.h"
 
diff --git a/cartographer/mapping/internal/3d/scan_matching/real_time_correlative_scan_matcher_3d.h b/cartographer/mapping/internal/3d/scan_matching/real_time_correlative_scan_matcher_3d.h
index 85af508..bf23377 100644
--- a/cartographer/mapping/internal/3d/scan_matching/real_time_correlative_scan_matcher_3d.h
+++ b/cartographer/mapping/internal/3d/scan_matching/real_time_correlative_scan_matcher_3d.h
@@ -21,7 +21,7 @@
 
 #include "Eigen/Core"
 #include "cartographer/mapping/3d/hybrid_grid.h"
-#include "cartographer/mapping/scan_matching/proto/real_time_correlative_scan_matcher_options.pb.h"
+#include "cartographer/mapping/proto/scan_matching/real_time_correlative_scan_matcher_options.pb.h"
 #include "cartographer/sensor/point_cloud.h"
 
 namespace cartographer {
diff --git a/cartographer/mapping/internal/constraints/constraint_builder.h b/cartographer/mapping/internal/constraints/constraint_builder.h
index 2c4e5e0..7532b17 100644
--- a/cartographer/mapping/internal/constraints/constraint_builder.h
+++ b/cartographer/mapping/internal/constraints/constraint_builder.h
@@ -18,7 +18,7 @@
 #define CARTOGRAPHER_MAPPING_INTERNAL_CONSTRAINTS_CONSTRAINT_BUILDER_H_
 
 #include "cartographer/common/lua_parameter_dictionary.h"
-#include "cartographer/mapping/pose_graph/proto/constraint_builder_options.pb.h"
+#include "cartographer/mapping/proto/pose_graph/constraint_builder_options.pb.h"
 
 namespace cartographer {
 namespace mapping {
diff --git a/cartographer/mapping/internal/constraints/constraint_builder_2d.cc b/cartographer/mapping/internal/constraints/constraint_builder_2d.cc
index de67b6f..c621385 100644
--- a/cartographer/mapping/internal/constraints/constraint_builder_2d.cc
+++ b/cartographer/mapping/internal/constraints/constraint_builder_2d.cc
@@ -29,8 +29,8 @@
 #include "cartographer/common/make_unique.h"
 #include "cartographer/common/math.h"
 #include "cartographer/common/thread_pool.h"
-#include "cartographer/mapping/2d/scan_matching/proto/ceres_scan_matcher_options_2d.pb.h"
-#include "cartographer/mapping/2d/scan_matching/proto/fast_correlative_scan_matcher_options_2d.pb.h"
+#include "cartographer/mapping/proto/scan_matching//ceres_scan_matcher_options_2d.pb.h"
+#include "cartographer/mapping/proto/scan_matching//fast_correlative_scan_matcher_options_2d.pb.h"
 #include "cartographer/metrics/counter.h"
 #include "cartographer/metrics/gauge.h"
 #include "cartographer/metrics/histogram.h"
diff --git a/cartographer/mapping/internal/constraints/constraint_builder_2d.h b/cartographer/mapping/internal/constraints/constraint_builder_2d.h
index 5ac1e55..aeb3f49 100644
--- a/cartographer/mapping/internal/constraints/constraint_builder_2d.h
+++ b/cartographer/mapping/internal/constraints/constraint_builder_2d.h
@@ -34,8 +34,8 @@
 #include "cartographer/mapping/2d/submap_2d.h"
 #include "cartographer/mapping/internal/2d/scan_matching/ceres_scan_matcher_2d.h"
 #include "cartographer/mapping/internal/2d/scan_matching/fast_correlative_scan_matcher_2d.h"
-#include "cartographer/mapping/pose_graph/proto/constraint_builder_options.pb.h"
 #include "cartographer/mapping/pose_graph_interface.h"
+#include "cartographer/mapping/proto/pose_graph/constraint_builder_options.pb.h"
 #include "cartographer/metrics/family_factory.h"
 #include "cartographer/sensor/internal/voxel_filter.h"
 #include "cartographer/sensor/point_cloud.h"
diff --git a/cartographer/mapping/internal/constraints/constraint_builder_3d.cc b/cartographer/mapping/internal/constraints/constraint_builder_3d.cc
index 99361ed..8510631 100644
--- a/cartographer/mapping/internal/constraints/constraint_builder_3d.cc
+++ b/cartographer/mapping/internal/constraints/constraint_builder_3d.cc
@@ -29,8 +29,8 @@
 #include "cartographer/common/make_unique.h"
 #include "cartographer/common/math.h"
 #include "cartographer/common/thread_pool.h"
-#include "cartographer/mapping/3d/scan_matching/proto/ceres_scan_matcher_options_3d.pb.h"
-#include "cartographer/mapping/3d/scan_matching/proto/fast_correlative_scan_matcher_options_3d.pb.h"
+#include "cartographer/mapping/proto/scan_matching//ceres_scan_matcher_options_3d.pb.h"
+#include "cartographer/mapping/proto/scan_matching//fast_correlative_scan_matcher_options_3d.pb.h"
 #include "cartographer/metrics/counter.h"
 #include "cartographer/metrics/gauge.h"
 #include "cartographer/metrics/histogram.h"
diff --git a/cartographer/mapping/internal/constraints/constraint_builder_3d.h b/cartographer/mapping/internal/constraints/constraint_builder_3d.h
index 37262ed..8b81131 100644
--- a/cartographer/mapping/internal/constraints/constraint_builder_3d.h
+++ b/cartographer/mapping/internal/constraints/constraint_builder_3d.h
@@ -35,8 +35,8 @@
 #include "cartographer/mapping/3d/submap_3d.h"
 #include "cartographer/mapping/internal/3d/scan_matching/ceres_scan_matcher_3d.h"
 #include "cartographer/mapping/internal/3d/scan_matching/fast_correlative_scan_matcher_3d.h"
-#include "cartographer/mapping/pose_graph/proto/constraint_builder_options.pb.h"
 #include "cartographer/mapping/pose_graph_interface.h"
+#include "cartographer/mapping/proto/pose_graph/constraint_builder_options.pb.h"
 #include "cartographer/mapping/trajectory_node.h"
 #include "cartographer/metrics/family_factory.h"
 #include "cartographer/sensor/compressed_point_cloud.h"
diff --git a/cartographer/mapping/internal/optimization/optimization_problem_2d.h b/cartographer/mapping/internal/optimization/optimization_problem_2d.h
index f5094d9..d968d6f 100644
--- a/cartographer/mapping/internal/optimization/optimization_problem_2d.h
+++ b/cartographer/mapping/internal/optimization/optimization_problem_2d.h
@@ -29,8 +29,8 @@
 #include "cartographer/common/time.h"
 #include "cartographer/mapping/id.h"
 #include "cartographer/mapping/internal/optimization/optimization_problem_interface.h"
-#include "cartographer/mapping/pose_graph/proto/optimization_problem_options.pb.h"
 #include "cartographer/mapping/pose_graph_interface.h"
+#include "cartographer/mapping/proto/pose_graph/optimization_problem_options.pb.h"
 #include "cartographer/sensor/imu_data.h"
 #include "cartographer/sensor/map_by_time.h"
 #include "cartographer/sensor/odometry_data.h"
diff --git a/cartographer/mapping/internal/optimization/optimization_problem_3d.h b/cartographer/mapping/internal/optimization/optimization_problem_3d.h
index db1a475..0f6453d 100644
--- a/cartographer/mapping/internal/optimization/optimization_problem_3d.h
+++ b/cartographer/mapping/internal/optimization/optimization_problem_3d.h
@@ -29,8 +29,8 @@
 #include "cartographer/common/time.h"
 #include "cartographer/mapping/id.h"
 #include "cartographer/mapping/internal/optimization/optimization_problem_interface.h"
-#include "cartographer/mapping/pose_graph/proto/optimization_problem_options.pb.h"
 #include "cartographer/mapping/pose_graph_interface.h"
+#include "cartographer/mapping/proto/pose_graph/optimization_problem_options.pb.h"
 #include "cartographer/sensor/fixed_frame_pose_data.h"
 #include "cartographer/sensor/imu_data.h"
 #include "cartographer/sensor/map_by_time.h"
diff --git a/cartographer/mapping/internal/optimization/optimization_problem_options.h b/cartographer/mapping/internal/optimization/optimization_problem_options.h
index 5182760..5351e39 100644
--- a/cartographer/mapping/internal/optimization/optimization_problem_options.h
+++ b/cartographer/mapping/internal/optimization/optimization_problem_options.h
@@ -18,7 +18,7 @@
 #define CARTOGRAPHER_MAPPING_INTERNAL_OPTIMIZATION_OPTIMIZATION_PROBLEM_OPTIONS_H_
 
 #include "cartographer/common/lua_parameter_dictionary.h"
-#include "cartographer/mapping/pose_graph/proto/optimization_problem_options.pb.h"
+#include "cartographer/mapping/proto/pose_graph/optimization_problem_options.pb.h"
 
 namespace cartographer {
 namespace mapping {
diff --git a/cartographer/mapping/internal/scan_matching/real_time_correlative_scan_matcher.h b/cartographer/mapping/internal/scan_matching/real_time_correlative_scan_matcher.h
index 2345dfc..47d3d01 100644
--- a/cartographer/mapping/internal/scan_matching/real_time_correlative_scan_matcher.h
+++ b/cartographer/mapping/internal/scan_matching/real_time_correlative_scan_matcher.h
@@ -19,7 +19,7 @@
 #define CARTOGRAPHER_MAPPING_INTERNAL_SCAN_MATCHING_REAL_TIME_CORRELATIVE_SCAN_MATCHER_H_
 
 #include "cartographer/common/lua_parameter_dictionary.h"
-#include "cartographer/mapping/scan_matching/proto/real_time_correlative_scan_matcher_options.pb.h"
+#include "cartographer/mapping/proto/scan_matching/real_time_correlative_scan_matcher_options.pb.h"
 
 namespace cartographer {
 namespace mapping {
diff --git a/cartographer/mapping/2d/proto/cell_limits.proto b/cartographer/mapping/proto/2d/cell_limits.proto
similarity index 100%
rename from cartographer/mapping/2d/proto/cell_limits.proto
rename to cartographer/mapping/proto/2d/cell_limits.proto
diff --git a/cartographer/mapping/2d/proto/grid_2d.proto b/cartographer/mapping/proto/2d/grid_2d.proto
similarity index 90%
rename from cartographer/mapping/2d/proto/grid_2d.proto
rename to cartographer/mapping/proto/2d/grid_2d.proto
index c6a0e2c..152c719 100644
--- a/cartographer/mapping/2d/proto/grid_2d.proto
+++ b/cartographer/mapping/proto/2d/grid_2d.proto
@@ -16,8 +16,8 @@ syntax = "proto3";
 
 package cartographer.mapping.proto;
 
-import "cartographer/mapping/2d/proto/probability_grid.proto";
-import "cartographer/mapping/2d/proto/map_limits.proto";
+import "cartographer/mapping/proto/2d/map_limits.proto";
+import "cartographer/mapping/proto/2d/probability_grid.proto";
 
 message Grid2D {
   message CellBox {
diff --git a/cartographer/mapping/2d/proto/grid_2d_options.proto b/cartographer/mapping/proto/2d/grid_2d_options.proto
similarity index 100%
rename from cartographer/mapping/2d/proto/grid_2d_options.proto
rename to cartographer/mapping/proto/2d/grid_2d_options.proto
diff --git a/cartographer/mapping/2d/proto/local_trajectory_builder_options_2d.proto b/cartographer/mapping/proto/2d/local_trajectory_builder_options_2d.proto
similarity index 92%
rename from cartographer/mapping/2d/proto/local_trajectory_builder_options_2d.proto
rename to cartographer/mapping/proto/2d/local_trajectory_builder_options_2d.proto
index 1c9a91c..2189091 100644
--- a/cartographer/mapping/2d/proto/local_trajectory_builder_options_2d.proto
+++ b/cartographer/mapping/proto/2d/local_trajectory_builder_options_2d.proto
@@ -18,9 +18,9 @@ package cartographer.mapping.proto;
 
 import "cartographer/mapping/proto/motion_filter_options.proto";
 import "cartographer/sensor/proto/adaptive_voxel_filter_options.proto";
-import "cartographer/mapping/2d/proto/submaps_options_2d.proto";
-import "cartographer/mapping/2d/scan_matching/proto/ceres_scan_matcher_options_2d.proto";
-import "cartographer/mapping/scan_matching/proto/real_time_correlative_scan_matcher_options.proto";
+import "cartographer/mapping/proto/2d/submaps_options_2d.proto";
+import "cartographer/mapping/proto/scan_matching/ceres_scan_matcher_options_2d.proto";
+import "cartographer/mapping/proto/scan_matching/real_time_correlative_scan_matcher_options.proto";
 
 message LocalTrajectoryBuilderOptions2D {
   // Rangefinder points outside these ranges will be dropped.
diff --git a/cartographer/mapping/2d/proto/map_limits.proto b/cartographer/mapping/proto/2d/map_limits.proto
similarity index 93%
rename from cartographer/mapping/2d/proto/map_limits.proto
rename to cartographer/mapping/proto/2d/map_limits.proto
index 20bd883..56f0a99 100644
--- a/cartographer/mapping/2d/proto/map_limits.proto
+++ b/cartographer/mapping/proto/2d/map_limits.proto
@@ -14,7 +14,7 @@
 
 syntax = "proto3";
 
-import "cartographer/mapping/2d/proto/cell_limits.proto";
+import "cartographer/mapping/proto/2d/cell_limits.proto";
 import "cartographer/transform/proto/transform.proto";
 
 package cartographer.mapping.proto;
diff --git a/cartographer/mapping/2d/proto/probability_grid.proto b/cartographer/mapping/proto/2d/probability_grid.proto
similarity index 100%
rename from cartographer/mapping/2d/proto/probability_grid.proto
rename to cartographer/mapping/proto/2d/probability_grid.proto
diff --git a/cartographer/mapping/2d/proto/probability_grid_range_data_inserter_options_2d.proto b/cartographer/mapping/proto/2d/probability_grid_range_data_inserter_options_2d.proto
similarity index 100%
rename from cartographer/mapping/2d/proto/probability_grid_range_data_inserter_options_2d.proto
rename to cartographer/mapping/proto/2d/probability_grid_range_data_inserter_options_2d.proto
diff --git a/cartographer/mapping/2d/proto/submaps_options_2d.proto b/cartographer/mapping/proto/2d/submaps_options_2d.proto
similarity index 87%
rename from cartographer/mapping/2d/proto/submaps_options_2d.proto
rename to cartographer/mapping/proto/2d/submaps_options_2d.proto
index 7826716..ebb3c58 100644
--- a/cartographer/mapping/2d/proto/submaps_options_2d.proto
+++ b/cartographer/mapping/proto/2d/submaps_options_2d.proto
@@ -14,8 +14,7 @@
 
 syntax = "proto3";
 
-import "cartographer/mapping/2d/proto/grid_2d_options.proto";
-import "cartographer/mapping/2d/proto/probability_grid_range_data_inserter_options_2d.proto";
+import "cartographer/mapping/proto/2d/grid_2d_options.proto";
 import "cartographer/mapping/proto/range_data_inserter_options.proto";
 
 package cartographer.mapping.proto;
diff --git a/cartographer/mapping/3d/proto/hybrid_grid.proto b/cartographer/mapping/proto/3d/hybrid_grid.proto
similarity index 100%
rename from cartographer/mapping/3d/proto/hybrid_grid.proto
rename to cartographer/mapping/proto/3d/hybrid_grid.proto
diff --git a/cartographer/mapping/3d/proto/local_trajectory_builder_options_3d.proto b/cartographer/mapping/proto/3d/local_trajectory_builder_options_3d.proto
similarity index 92%
rename from cartographer/mapping/3d/proto/local_trajectory_builder_options_3d.proto
rename to cartographer/mapping/proto/3d/local_trajectory_builder_options_3d.proto
index 42d6b31..5bdd4f2 100644
--- a/cartographer/mapping/3d/proto/local_trajectory_builder_options_3d.proto
+++ b/cartographer/mapping/proto/3d/local_trajectory_builder_options_3d.proto
@@ -16,11 +16,11 @@ syntax = "proto3";
 
 package cartographer.mapping.proto;
 
+import "cartographer/mapping/proto/3d/submaps_options_3d.proto";
 import "cartographer/mapping/proto/motion_filter_options.proto";
+import "cartographer/mapping/proto/scan_matching/ceres_scan_matcher_options_3d.proto";
+import "cartographer/mapping/proto/scan_matching/real_time_correlative_scan_matcher_options.proto";
 import "cartographer/sensor/proto/adaptive_voxel_filter_options.proto";
-import "cartographer/mapping/scan_matching/proto/real_time_correlative_scan_matcher_options.proto";
-import "cartographer/mapping/3d/proto/submaps_options_3d.proto";
-import "cartographer/mapping/3d/scan_matching/proto/ceres_scan_matcher_options_3d.proto";
 
 // NEXT ID: 18
 message LocalTrajectoryBuilderOptions3D {
diff --git a/cartographer/mapping/3d/proto/range_data_inserter_options_3d.proto b/cartographer/mapping/proto/3d/range_data_inserter_options_3d.proto
similarity index 100%
rename from cartographer/mapping/3d/proto/range_data_inserter_options_3d.proto
rename to cartographer/mapping/proto/3d/range_data_inserter_options_3d.proto
diff --git a/cartographer/mapping/3d/proto/submaps_options_3d.proto b/cartographer/mapping/proto/3d/submaps_options_3d.proto
similarity index 95%
rename from cartographer/mapping/3d/proto/submaps_options_3d.proto
rename to cartographer/mapping/proto/3d/submaps_options_3d.proto
index 27a6813..29b4db8 100644
--- a/cartographer/mapping/3d/proto/submaps_options_3d.proto
+++ b/cartographer/mapping/proto/3d/submaps_options_3d.proto
@@ -14,7 +14,7 @@
 
 syntax = "proto3";
 
-import "cartographer/mapping/3d/proto/range_data_inserter_options_3d.proto";
+import "cartographer/mapping/proto/3d/range_data_inserter_options_3d.proto";
 
 package cartographer.mapping.proto;
 
diff --git a/cartographer/mapping/pose_graph/proto/constraint_builder_options.proto b/cartographer/mapping/proto/pose_graph/constraint_builder_options.proto
similarity index 84%
rename from cartographer/mapping/pose_graph/proto/constraint_builder_options.proto
rename to cartographer/mapping/proto/pose_graph/constraint_builder_options.proto
index b4b0af8..8447cba 100644
--- a/cartographer/mapping/pose_graph/proto/constraint_builder_options.proto
+++ b/cartographer/mapping/proto/pose_graph/constraint_builder_options.proto
@@ -16,10 +16,10 @@ syntax = "proto3";
 
 package cartographer.mapping.constraints.proto;
 
-import "cartographer/mapping/2d/scan_matching/proto/ceres_scan_matcher_options_2d.proto";
-import "cartographer/mapping/2d/scan_matching/proto/fast_correlative_scan_matcher_options_2d.proto";
-import "cartographer/mapping/3d/scan_matching/proto/ceres_scan_matcher_options_3d.proto";
-import "cartographer/mapping/3d/scan_matching/proto/fast_correlative_scan_matcher_options_3d.proto";
+import "cartographer/mapping/proto/scan_matching/ceres_scan_matcher_options_2d.proto";
+import "cartographer/mapping/proto/scan_matching/ceres_scan_matcher_options_3d.proto";
+import "cartographer/mapping/proto/scan_matching/fast_correlative_scan_matcher_options_2d.proto";
+import "cartographer/mapping/proto/scan_matching/fast_correlative_scan_matcher_options_3d.proto";
 
 message ConstraintBuilderOptions {
   // A constraint will be added if the proportion of added constraints to
diff --git a/cartographer/mapping/pose_graph/proto/optimization_problem_options.proto b/cartographer/mapping/proto/pose_graph/optimization_problem_options.proto
similarity index 100%
rename from cartographer/mapping/pose_graph/proto/optimization_problem_options.proto
rename to cartographer/mapping/proto/pose_graph/optimization_problem_options.proto
diff --git a/cartographer/mapping/proto/pose_graph_options.proto b/cartographer/mapping/proto/pose_graph_options.proto
index a5fe889..14d08c5 100644
--- a/cartographer/mapping/proto/pose_graph_options.proto
+++ b/cartographer/mapping/proto/pose_graph_options.proto
@@ -16,8 +16,8 @@ syntax = "proto3";
 
 package cartographer.mapping.proto;
 
-import "cartographer/mapping/pose_graph/proto/constraint_builder_options.proto";
-import "cartographer/mapping/pose_graph/proto/optimization_problem_options.proto";
+import "cartographer/mapping/proto/pose_graph/constraint_builder_options.proto";
+import "cartographer/mapping/proto/pose_graph/optimization_problem_options.proto";
 
 message PoseGraphOptions {
   // Online loop closure: If positive, will run the loop closure while the map
diff --git a/cartographer/mapping/proto/range_data_inserter_options.proto b/cartographer/mapping/proto/range_data_inserter_options.proto
index ff68263..f0be593 100644
--- a/cartographer/mapping/proto/range_data_inserter_options.proto
+++ b/cartographer/mapping/proto/range_data_inserter_options.proto
@@ -14,7 +14,7 @@
 
 syntax = "proto3";
 
-import "cartographer/mapping/2d/proto/probability_grid_range_data_inserter_options_2d.proto";
+import "cartographer/mapping/proto/2d/probability_grid_range_data_inserter_options_2d.proto";
 
 package cartographer.mapping.proto;
 
diff --git a/cartographer/mapping/2d/scan_matching/proto/ceres_scan_matcher_options_2d.proto b/cartographer/mapping/proto/scan_matching/ceres_scan_matcher_options_2d.proto
similarity index 100%
rename from cartographer/mapping/2d/scan_matching/proto/ceres_scan_matcher_options_2d.proto
rename to cartographer/mapping/proto/scan_matching/ceres_scan_matcher_options_2d.proto
diff --git a/cartographer/mapping/3d/scan_matching/proto/ceres_scan_matcher_options_3d.proto b/cartographer/mapping/proto/scan_matching/ceres_scan_matcher_options_3d.proto
similarity index 100%
rename from cartographer/mapping/3d/scan_matching/proto/ceres_scan_matcher_options_3d.proto
rename to cartographer/mapping/proto/scan_matching/ceres_scan_matcher_options_3d.proto
diff --git a/cartographer/mapping/2d/scan_matching/proto/fast_correlative_scan_matcher_options_2d.proto b/cartographer/mapping/proto/scan_matching/fast_correlative_scan_matcher_options_2d.proto
similarity index 100%
rename from cartographer/mapping/2d/scan_matching/proto/fast_correlative_scan_matcher_options_2d.proto
rename to cartographer/mapping/proto/scan_matching/fast_correlative_scan_matcher_options_2d.proto
diff --git a/cartographer/mapping/3d/scan_matching/proto/fast_correlative_scan_matcher_options_3d.proto b/cartographer/mapping/proto/scan_matching/fast_correlative_scan_matcher_options_3d.proto
similarity index 100%
rename from cartographer/mapping/3d/scan_matching/proto/fast_correlative_scan_matcher_options_3d.proto
rename to cartographer/mapping/proto/scan_matching/fast_correlative_scan_matcher_options_3d.proto
diff --git a/cartographer/mapping/scan_matching/proto/real_time_correlative_scan_matcher_options.proto b/cartographer/mapping/proto/scan_matching/real_time_correlative_scan_matcher_options.proto
similarity index 100%
rename from cartographer/mapping/scan_matching/proto/real_time_correlative_scan_matcher_options.proto
rename to cartographer/mapping/proto/scan_matching/real_time_correlative_scan_matcher_options.proto
diff --git a/cartographer/mapping/proto/submap.proto b/cartographer/mapping/proto/submap.proto
index 75e1a12..6fab2c4 100644
--- a/cartographer/mapping/proto/submap.proto
+++ b/cartographer/mapping/proto/submap.proto
@@ -16,8 +16,8 @@ syntax = "proto3";
 
 package cartographer.mapping.proto;
 
-import "cartographer/mapping/2d/proto/grid_2d.proto";
-import "cartographer/mapping/3d/proto/hybrid_grid.proto";
+import "cartographer/mapping/proto/2d/grid_2d.proto";
+import "cartographer/mapping/proto/3d/hybrid_grid.proto";
 import "cartographer/transform/proto/transform.proto";
 
 // Serialized state of a Submap2D.
diff --git a/cartographer/mapping/proto/trajectory_builder_options.proto b/cartographer/mapping/proto/trajectory_builder_options.proto
index 489a194..6c07eb9 100644
--- a/cartographer/mapping/proto/trajectory_builder_options.proto
+++ b/cartographer/mapping/proto/trajectory_builder_options.proto
@@ -15,8 +15,8 @@
 syntax = "proto3";
 
 import "cartographer/transform/proto/transform.proto";
-import "cartographer/mapping/2d/proto/local_trajectory_builder_options_2d.proto";
-import "cartographer/mapping/3d/proto/local_trajectory_builder_options_3d.proto";
+import "cartographer/mapping/proto/2d/local_trajectory_builder_options_2d.proto";
+import "cartographer/mapping/proto/3d/local_trajectory_builder_options_3d.proto";
 
 package cartographer.mapping.proto;
 
diff --git a/cartographer/mapping/range_data_inserter_interface.h b/cartographer/mapping/range_data_inserter_interface.h
index b0074ca..b9051ef 100644
--- a/cartographer/mapping/range_data_inserter_interface.h
+++ b/cartographer/mapping/range_data_inserter_interface.h
@@ -20,8 +20,8 @@
 #include <utility>
 #include <vector>
 
-#include "cartographer/mapping/2d/proto/submaps_options_2d.pb.h"
 #include "cartographer/mapping/grid_interface.h"
+#include "cartographer/mapping/proto/2d/submaps_options_2d.pb.h"
 #include "cartographer/sensor/range_data.h"
 
 namespace cartographer {