diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1b138752ed..dd804eb588 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -64,7 +64,7 @@ repos:
         - --linelength=240
         # https://google.github.io/styleguide/cppguide.html
         # relevant rules are whitelisted, see all options with: cpplint --filter=
-        - --filter=-build,-legal,-readability,-runtime,-whitespace,+build/forward_decl,+build/include_what_you_use,+build/deprecated,+whitespace/line_length,+whitespace/empty_if_body,+whitespace/empty_loop_body,+whitespace/empty_conditional_body,+whitespace/forcolon,+whitespace/parens,+whitespace/semicolon,+readability/braces
+        - --filter=-build,-legal,-readability,-runtime,-whitespace,+build/include_subdir,+build/forward_decl,+build/include_what_you_use,+build/deprecated,+whitespace/line_length,+whitespace/empty_if_body,+whitespace/empty_loop_body,+whitespace/empty_conditional_body,+whitespace/forcolon,+whitespace/parens,+whitespace/semicolon,+readability/braces
 -   repo: local
     hooks:
     -   id: test_translations
diff --git a/common/swaglog.cc b/common/swaglog.cc
index c0614c85f5..923f701ab2 100644
--- a/common/swaglog.cc
+++ b/common/swaglog.cc
@@ -12,7 +12,7 @@
 #include <string>
 
 #include <zmq.h>
-#include "json11.hpp"
+#include "third_party/json11/json11.hpp"
 
 #include "common/util.h"
 #include "common/version.h"
diff --git a/common/tests/test_swaglog.cc b/common/tests/test_swaglog.cc
index 20455ec74c..021656a78b 100644
--- a/common/tests/test_swaglog.cc
+++ b/common/tests/test_swaglog.cc
@@ -3,7 +3,7 @@
 #define CATCH_CONFIG_MAIN
 #include "catch2/catch.hpp"
 
-#include "json11.hpp"
+#include "third_party/json11/json11.hpp"
 #include "common/swaglog.h"
 #include "common/util.h"
 #include "common/version.h"
diff --git a/common/transformations/coordinates.cc b/common/transformations/coordinates.cc
index b729ac3d87..5b00b53a4f 100644
--- a/common/transformations/coordinates.cc
+++ b/common/transformations/coordinates.cc
@@ -1,13 +1,11 @@
 #define _USE_MATH_DEFINES
 
+#include "common/transformations/coordinates.hpp"
+
 #include <iostream>
 #include <cmath>
 #include <eigen3/Eigen/Dense>
 
-#include "coordinates.hpp"
-
-
-
 double a = 6378137; // lgtm [cpp/short-global-name]
 double b = 6356752.3142; // lgtm [cpp/short-global-name]
 double esq = 6.69437999014 * 0.001; // lgtm [cpp/short-global-name]
diff --git a/common/transformations/coordinates.hpp b/common/transformations/coordinates.hpp
index f5ba0d3fe7..32ec2ff66e 100644
--- a/common/transformations/coordinates.hpp
+++ b/common/transformations/coordinates.hpp
@@ -1,5 +1,7 @@
 #pragma once
 
+#include <eigen3/Eigen/Dense>
+
 #define DEG2RAD(x) ((x) * M_PI / 180.0)
 #define RAD2DEG(x) ((x) * 180.0 / M_PI)
 
diff --git a/common/transformations/orientation.cc b/common/transformations/orientation.cc
index 7909c0affb..00888c3a92 100644
--- a/common/transformations/orientation.cc
+++ b/common/transformations/orientation.cc
@@ -4,8 +4,8 @@
 #include <cmath>
 #include <eigen3/Eigen/Dense>
 
-#include "orientation.hpp"
-#include "coordinates.hpp"
+#include "common/transformations/orientation.hpp"
+#include "common/transformations/coordinates.hpp"
 
 Eigen::Quaterniond ensure_unique(Eigen::Quaterniond quat){
   if (quat.w() > 0){
diff --git a/common/transformations/orientation.hpp b/common/transformations/orientation.hpp
index ebd7da0aee..150b12cade 100644
--- a/common/transformations/orientation.hpp
+++ b/common/transformations/orientation.hpp
@@ -1,6 +1,6 @@
 #pragma once
 #include <eigen3/Eigen/Dense>
-#include "coordinates.hpp"
+#include "common/transformations/coordinates.hpp"
 
 
 Eigen::Quaterniond ensure_unique(Eigen::Quaterniond quat);
diff --git a/selfdrive/boardd/can_list_to_can_capnp.cc b/selfdrive/boardd/can_list_to_can_capnp.cc
index c1778c51a2..72ca72688a 100644
--- a/selfdrive/boardd/can_list_to_can_capnp.cc
+++ b/selfdrive/boardd/can_list_to_can_capnp.cc
@@ -1,5 +1,5 @@
 #include "cereal/messaging/messaging.h"
-#include "panda.h"
+#include "selfdrive/boardd/panda.h"
 
 void can_list_to_can_capnp_cpp(const std::vector<can_frame> &can_list, std::string &out, bool sendCan, bool valid) {
   MessageBuilder msg;
diff --git a/selfdrive/locationd/liblocationd.cc b/selfdrive/locationd/liblocationd.cc
index 6f298deab6..e2b85d93a1 100755
--- a/selfdrive/locationd/liblocationd.cc
+++ b/selfdrive/locationd/liblocationd.cc
@@ -1,4 +1,4 @@
-#include "locationd.h"
+#include "selfdrive/locationd/locationd.h"
 
 extern "C" {
   typedef Localizer* Localizer_t;
diff --git a/selfdrive/locationd/locationd.cc b/selfdrive/locationd/locationd.cc
index 722ead7dd4..3a4286a18b 100755
--- a/selfdrive/locationd/locationd.cc
+++ b/selfdrive/locationd/locationd.cc
@@ -1,3 +1,5 @@
+#include "selfdrive/locationd/locationd.h"
+
 #include <sys/time.h>
 #include <sys/resource.h>
 
@@ -5,8 +7,6 @@
 #include <cmath>
 #include <vector>
 
-#include "locationd.h"
-
 using namespace EKFS;
 using namespace Eigen;
 
diff --git a/selfdrive/locationd/models/live_kf.cc b/selfdrive/locationd/models/live_kf.cc
index f8c03365e1..915d0fd360 100755
--- a/selfdrive/locationd/models/live_kf.cc
+++ b/selfdrive/locationd/models/live_kf.cc
@@ -1,4 +1,4 @@
-#include "live_kf.h"
+#include "selfdrive/locationd/models/live_kf.h"
 
 using namespace EKFS;
 using namespace Eigen;
diff --git a/selfdrive/modeld/runners/run.h b/selfdrive/modeld/runners/run.h
index c64f300fe2..7f6e1aa569 100644
--- a/selfdrive/modeld/runners/run.h
+++ b/selfdrive/modeld/runners/run.h
@@ -1,10 +1,10 @@
 #pragma once
 
-#include "runmodel.h"
-#include "snpemodel.h"
+#include "selfdrive/modeld/runners/runmodel.h"
+#include "selfdrive/modeld/runners/snpemodel.h"
 
 #if defined(USE_THNEED)
-#include "thneedmodel.h"
+#include "selfdrive/modeld/runners/thneedmodel.h"
 #elif defined(USE_ONNX_MODEL)
-#include "onnxmodel.h"
+#include "selfdrive/modeld/runners/onnxmodel.h"
 #endif
diff --git a/selfdrive/modeld/thneed/serialize.cc b/selfdrive/modeld/thneed/serialize.cc
index 51e6d08699..6ed5c08e81 100644
--- a/selfdrive/modeld/thneed/serialize.cc
+++ b/selfdrive/modeld/thneed/serialize.cc
@@ -1,7 +1,7 @@
 #include <cassert>
 #include <set>
 
-#include "json11.hpp"
+#include "third_party/json11/json11.hpp"
 #include "common/util.h"
 #include "common/clutil.h"
 #include "selfdrive/modeld/thneed/thneed.h"
diff --git a/selfdrive/modeld/thneed/thneed.h b/selfdrive/modeld/thneed/thneed.h
index 6475577734..47e18e0be3 100644
--- a/selfdrive/modeld/thneed/thneed.h
+++ b/selfdrive/modeld/thneed/thneed.h
@@ -12,7 +12,7 @@
 
 #include <CL/cl.h>
 
-#include "msm_kgsl.h"
+#include "third_party/linux/include/msm_kgsl.h"
 
 using namespace std;
 
diff --git a/selfdrive/ui/qt/maps/map_settings.cc b/selfdrive/ui/qt/maps/map_settings.cc
index 48a7733c52..a4386ded72 100644
--- a/selfdrive/ui/qt/maps/map_settings.cc
+++ b/selfdrive/ui/qt/maps/map_settings.cc
@@ -1,4 +1,4 @@
-#include "map_settings.h"
+#include "selfdrive/ui/qt/maps/map_settings.h"
 
 #include <utility>
 
diff --git a/system/camerad/cameras/camera_common.cc b/system/camerad/cameras/camera_common.cc
index 1eb636b7a2..23b28357da 100644
--- a/system/camerad/cameras/camera_common.cc
+++ b/system/camerad/cameras/camera_common.cc
@@ -8,7 +8,7 @@
 #include <string>
 #include <thread>
 
-#include "libyuv.h"
+#include "third_party/libyuv/include/libyuv.h"
 #include <jpeglib.h>
 
 #include "system/camerad/imgproc/utils.h"
@@ -17,7 +17,7 @@
 #include "common/swaglog.h"
 #include "common/util.h"
 #include "system/hardware/hw.h"
-#include "msm_media_info.h"
+#include "third_party/linux/include/msm_media_info.h"
 
 #include "system/camerad/cameras/camera_qcom2.h"
 #ifdef QCOM2
diff --git a/system/camerad/test/ae_gray_test.cc b/system/camerad/test/ae_gray_test.cc
index aabd7534ee..8d18f7e93b 100644
--- a/system/camerad/test/ae_gray_test.cc
+++ b/system/camerad/test/ae_gray_test.cc
@@ -1,6 +1,6 @@
 // unittest for set_exposure_target
 
-#include "ae_gray_test.h"
+#include "system/camerad/test/ae_gray_test.h"
 
 #include <cassert>
 
diff --git a/system/logcatd/logcatd_systemd.cc b/system/logcatd/logcatd_systemd.cc
index 721726ed27..54b3782132 100644
--- a/system/logcatd/logcatd_systemd.cc
+++ b/system/logcatd/logcatd_systemd.cc
@@ -5,7 +5,7 @@
 #include <map>
 #include <string>
 
-#include "json11.hpp"
+#include "third_party/json11/json11.hpp"
 
 #include "cereal/messaging/messaging.h"
 #include "common/timing.h"
diff --git a/system/loggerd/encoder/ffmpeg_encoder.cc b/system/loggerd/encoder/ffmpeg_encoder.cc
index b73f4e8f5d..dc20ea8791 100644
--- a/system/loggerd/encoder/ffmpeg_encoder.cc
+++ b/system/loggerd/encoder/ffmpeg_encoder.cc
@@ -11,7 +11,7 @@
 
 #define __STDC_CONSTANT_MACROS
 
-#include "libyuv.h"
+#include "third_party/libyuv/include/libyuv.h"
 
 extern "C" {
 #include <libavcodec/avcodec.h>
diff --git a/system/loggerd/encoder/v4l_encoder.cc b/system/loggerd/encoder/v4l_encoder.cc
index 2f74c3785a..b09fa1e6ba 100644
--- a/system/loggerd/encoder/v4l_encoder.cc
+++ b/system/loggerd/encoder/v4l_encoder.cc
@@ -7,11 +7,11 @@
 #include "common/util.h"
 #include "common/timing.h"
 
-#include "libyuv.h"
-#include "msm_media_info.h"
+#include "third_party/libyuv/include/libyuv.h"
+#include "third_party/linux/include/msm_media_info.h"
 
 // has to be in this order
-#include "v4l2-controls.h"
+#include "third_party/linux/include/v4l2-controls.h"
 #include <linux/videodev2.h>
 #define V4L2_QCOM_BUF_FLAG_CODECCONFIG 0x00020000
 #define V4L2_QCOM_BUF_FLAG_EOS 0x02000000
diff --git a/system/sensord/sensors/bmx055_accel.cc b/system/sensord/sensors/bmx055_accel.cc
index 0c48d1e3ba..bdb0113de3 100644
--- a/system/sensord/sensors/bmx055_accel.cc
+++ b/system/sensord/sensors/bmx055_accel.cc
@@ -1,4 +1,4 @@
-#include "bmx055_accel.h"
+#include "system/sensord/sensors/bmx055_accel.h"
 
 #include <cassert>
 
diff --git a/system/sensord/sensors/bmx055_gyro.cc b/system/sensord/sensors/bmx055_gyro.cc
index ba41f3b47c..411b2f445e 100644
--- a/system/sensord/sensors/bmx055_gyro.cc
+++ b/system/sensord/sensors/bmx055_gyro.cc
@@ -1,4 +1,4 @@
-#include "bmx055_gyro.h"
+#include "system/sensord/sensors/bmx055_gyro.h"
 
 #include <cassert>
 #include <cmath>
diff --git a/system/sensord/sensors/bmx055_magn.cc b/system/sensord/sensors/bmx055_magn.cc
index 950e608923..585bf1b2d2 100644
--- a/system/sensord/sensors/bmx055_magn.cc
+++ b/system/sensord/sensors/bmx055_magn.cc
@@ -1,4 +1,4 @@
-#include "bmx055_magn.h"
+#include "system/sensord/sensors/bmx055_magn.h"
 
 #include <unistd.h>
 
diff --git a/system/sensord/sensors/bmx055_temp.cc b/system/sensord/sensors/bmx055_temp.cc
index 68ee0da1d6..da7b86476c 100644
--- a/system/sensord/sensors/bmx055_temp.cc
+++ b/system/sensord/sensors/bmx055_temp.cc
@@ -1,4 +1,4 @@
-#include "bmx055_temp.h"
+#include "system/sensord/sensors/bmx055_temp.h"
 
 #include <cassert>
 
diff --git a/system/sensord/sensors/i2c_sensor.cc b/system/sensord/sensors/i2c_sensor.cc
index f563f93d2b..90220f551d 100644
--- a/system/sensord/sensors/i2c_sensor.cc
+++ b/system/sensord/sensors/i2c_sensor.cc
@@ -1,4 +1,4 @@
-#include "i2c_sensor.h"
+#include "system/sensord/sensors/i2c_sensor.h"
 
 int16_t read_12_bit(uint8_t lsb, uint8_t msb) {
   uint16_t combined = (uint16_t(msb) << 8) | uint16_t(lsb & 0xF0);
diff --git a/system/sensord/sensors/lsm6ds3_accel.cc b/system/sensord/sensors/lsm6ds3_accel.cc
index 139b5df67a..03533e0657 100644
--- a/system/sensord/sensors/lsm6ds3_accel.cc
+++ b/system/sensord/sensors/lsm6ds3_accel.cc
@@ -1,4 +1,4 @@
-#include "lsm6ds3_accel.h"
+#include "system/sensord/sensors/lsm6ds3_accel.h"
 
 #include <cassert>
 #include <cmath>
diff --git a/system/sensord/sensors/lsm6ds3_gyro.cc b/system/sensord/sensors/lsm6ds3_gyro.cc
index e6bdc6c8a9..0459b6ad64 100644
--- a/system/sensord/sensors/lsm6ds3_gyro.cc
+++ b/system/sensord/sensors/lsm6ds3_gyro.cc
@@ -1,4 +1,4 @@
-#include "lsm6ds3_gyro.h"
+#include "system/sensord/sensors/lsm6ds3_gyro.h"
 
 #include <cassert>
 #include <cmath>
diff --git a/system/sensord/sensors/lsm6ds3_temp.cc b/system/sensord/sensors/lsm6ds3_temp.cc
index c2e2c83c1d..f481614154 100644
--- a/system/sensord/sensors/lsm6ds3_temp.cc
+++ b/system/sensord/sensors/lsm6ds3_temp.cc
@@ -1,4 +1,4 @@
-#include "lsm6ds3_temp.h"
+#include "system/sensord/sensors/lsm6ds3_temp.h"
 
 #include <cassert>
 
diff --git a/system/sensord/sensors/mmc5603nj_magn.cc b/system/sensord/sensors/mmc5603nj_magn.cc
index b69c602bdf..0e8ba967e3 100644
--- a/system/sensord/sensors/mmc5603nj_magn.cc
+++ b/system/sensord/sensors/mmc5603nj_magn.cc
@@ -1,4 +1,4 @@
-#include "mmc5603nj_magn.h"
+#include "system/sensord/sensors/mmc5603nj_magn.h"
 
 #include <algorithm>
 #include <cassert>
diff --git a/system/ubloxd/ublox_msg.cc b/system/ubloxd/ublox_msg.cc
index 48a39b7bef..7b4505dc81 100644
--- a/system/ubloxd/ublox_msg.cc
+++ b/system/ubloxd/ublox_msg.cc
@@ -1,4 +1,4 @@
-#include "ublox_msg.h"
+#include "system/ubloxd/ublox_msg.h"
 
 #include <unistd.h>
 
diff --git a/tools/cabana/streams/socketcanstream.cc b/tools/cabana/streams/socketcanstream.cc
index d5f9d115f2..3df8e31f3b 100644
--- a/tools/cabana/streams/socketcanstream.cc
+++ b/tools/cabana/streams/socketcanstream.cc
@@ -1,5 +1,4 @@
 #include "tools/cabana/streams/socketcanstream.h"
-#include "socketcanstream.h"
 
 #include <QLabel>
 #include <QMessageBox>
diff --git a/tools/lib/vidindex/bitstream.c b/tools/lib/vidindex/bitstream.c
index d174ffa8a7..dc6f43f14f 100644
--- a/tools/lib/vidindex/bitstream.c
+++ b/tools/lib/vidindex/bitstream.c
@@ -1,8 +1,8 @@
+#include "./bitstream.h"
+
 #include <stdbool.h>
 #include <assert.h>
 
-#include "bitstream.h"
-
 static const uint32_t BS_MASKS[33] = {
     0,           0x1L,        0x3L,       0x7L,       0xFL,       0x1FL,
     0x3FL,       0x7FL,       0xFFL,      0x1FFL,     0x3FFL,     0x7FFL,
diff --git a/tools/lib/vidindex/vidindex.c b/tools/lib/vidindex/vidindex.c
index 4857c60dd2..1d7da2e193 100644
--- a/tools/lib/vidindex/vidindex.c
+++ b/tools/lib/vidindex/vidindex.c
@@ -9,7 +9,7 @@
 #include <sys/stat.h>
 #include <sys/mman.h>
 
-#include "bitstream.h"
+#include "./bitstream.h"
 
 #define START_CODE 0x000001
 
diff --git a/tools/replay/camera.cc b/tools/replay/camera.cc
index 2bc8c66aaa..49f3010c6c 100644
--- a/tools/replay/camera.cc
+++ b/tools/replay/camera.cc
@@ -1,10 +1,11 @@
 #include "tools/replay/camera.h"
-#include "tools/replay/util.h"
-#include "msm_media_info.h"
 
 #include <cassert>
 #include <tuple>
 
+#include "third_party/linux/include/msm_media_info.h"
+#include "tools/replay/util.h"
+
 std::tuple<size_t, size_t, size_t> get_nv12_info(int width, int height) {
   int nv12_width = VENUS_Y_STRIDE(COLOR_FMT_NV12, width);
   int nv12_height = VENUS_Y_SCANLINES(COLOR_FMT_NV12, height);
diff --git a/tools/replay/framereader.cc b/tools/replay/framereader.cc
index f45996560e..303f0c60ca 100644
--- a/tools/replay/framereader.cc
+++ b/tools/replay/framereader.cc
@@ -3,7 +3,7 @@
 
 #include <cassert>
 #include <algorithm>
-#include "libyuv.h"
+#include "third_party/libyuv/include/libyuv.h"
 
 #ifdef __APPLE__
 #define HW_DEVICE_TYPE AV_HWDEVICE_TYPE_VIDEOTOOLBOX