diff --git a/vp9/common/arm/vp9_bilinearfilter_arm.c b/vp9/common/arm/vp9_bilinearfilter_arm.c
index 409e271b1..678173141 100644
--- a/vp9/common/arm/vp9_bilinearfilter_arm.c
+++ b/vp9/common/arm/vp9_bilinearfilter_arm.c
@@ -12,7 +12,7 @@
 #include <math.h>
 #include "vp9/common/vp9_filter.h"
 #include "vp9/common/vp9_subpixel.h"
-#include "vp9_bilinearfilter_arm.h"
+#include "vp9/common/arm/vp9_bilinearfilter_arm.h"
 
 void vp9_filter_block2d_bil_armv6
 (
diff --git a/vp9/common/ppc/vp9_loopfilter_altivec.c b/vp9/common/ppc/vp9_loopfilter_altivec.c
index cae171805..599070a75 100644
--- a/vp9/common/ppc/vp9_loopfilter_altivec.c
+++ b/vp9/common/ppc/vp9_loopfilter_altivec.c
@@ -9,8 +9,8 @@
  */
 
 
-#include "vp9_loopfilter.h"
-#include "vp9_onyxc_int.h"
+#include "vp9/common/vp9_loopfilter.h"
+#include "vp9/common/vp9_onyxc_int.h"
 
 typedef void loop_filter_function_y_ppc
 (
diff --git a/vp9/common/ppc/vp9_systemdependent.c b/vp9/common/ppc/vp9_systemdependent.c
index 2137dee9c..106a2b763 100644
--- a/vp9/common/ppc/vp9_systemdependent.c
+++ b/vp9/common/ppc/vp9_systemdependent.c
@@ -8,10 +8,10 @@
  *  be found in the AUTHORS file in the root of the source tree.
  */
 
-#include "vp9_subpixel.h"
-#include "vp9_loopfilter.h"
+#include "vp9/common/vp9_subpixel.h"
+#include "vp9/common/vp9_loopfilter.h"
 #include "recon.h"
-#include "vp9_onyxc_int.h"
+#include "vp9/common/vp9_onyxc_int.h"
 
 void (*vp8_short_idct4x4)(short *input, short *output, int pitch);
 void (*vp8_short_idct4x4_1)(short *input, short *output, int pitch);
diff --git a/vp9/common/vp9_alloccommon.c b/vp9/common/vp9_alloccommon.c
index 04a8b368a..08882b3a6 100644
--- a/vp9/common/vp9_alloccommon.c
+++ b/vp9/common/vp9_alloccommon.c
@@ -10,13 +10,13 @@
 
 
 #include "vpx_ports/config.h"
-#include "vp9_blockd.h"
+#include "vp9/common/vp9_blockd.h"
 #include "vpx_mem/vpx_mem.h"
-#include "vp9_onyxc_int.h"
-#include "vp9_findnearmv.h"
-#include "vp9_entropymode.h"
-#include "vp9_entropymv.h"
-#include "vp9_systemdependent.h"
+#include "vp9/common/vp9_onyxc_int.h"
+#include "vp9/common/vp9_findnearmv.h"
+#include "vp9/common/vp9_entropymode.h"
+#include "vp9/common/vp9_entropymv.h"
+#include "vp9/common/vp9_systemdependent.h"
 
 
 void vp9_update_mode_info_border(VP9_COMMON *cpi, MODE_INFO *mi_base) {
diff --git a/vp9/common/vp9_alloccommon.h b/vp9/common/vp9_alloccommon.h
index df94f421e..bfecef524 100644
--- a/vp9/common/vp9_alloccommon.h
+++ b/vp9/common/vp9_alloccommon.h
@@ -12,7 +12,7 @@
 #ifndef __INC_ALLOCCOMMON_H
 #define __INC_ALLOCCOMMON_H
 
-#include "vp9_onyxc_int.h"
+#include "vp9/common/vp9_onyxc_int.h"
 
 void vp9_create_common(VP9_COMMON *oci);
 void vp9_remove_common(VP9_COMMON *oci);
diff --git a/vp9/common/vp9_blockd.c b/vp9/common/vp9_blockd.c
index d8bb394d4..60aedf8cb 100644
--- a/vp9/common/vp9_blockd.c
+++ b/vp9/common/vp9_blockd.c
@@ -9,7 +9,7 @@
  */
 
 
-#include "vp9_blockd.h"
+#include "vp9/common/vp9_blockd.h"
 #include "vpx_mem/vpx_mem.h"
 
 
diff --git a/vp9/common/vp9_blockd.h b/vp9/common/vp9_blockd.h
index a91e8d4d0..d819a3d69 100644
--- a/vp9/common/vp9_blockd.h
+++ b/vp9/common/vp9_blockd.h
@@ -16,11 +16,11 @@ void vpx_log(const char *format, ...);
 
 #include "vpx_ports/config.h"
 #include "vpx_scale/yv12config.h"
-#include "vp9_mv.h"
-#include "vp9_treecoder.h"
-#include "vp9_subpixel.h"
+#include "vp9/common/vp9_mv.h"
+#include "vp9/common/vp9_treecoder.h"
+#include "vp9/common/vp9_subpixel.h"
 #include "vpx_ports/mem.h"
-#include "vp9_common.h"
+#include "vp9/common/vp9_common.h"
 
 #define TRUE    1
 #define FALSE   0
diff --git a/vp9/common/vp9_common.h b/vp9/common/vp9_common.h
index 61c0e25d8..64804e16e 100644
--- a/vp9/common/vp9_common.h
+++ b/vp9/common/vp9_common.h
@@ -18,7 +18,7 @@
 
 #include "vpx_mem/vpx_mem.h"
 
-#include "vp9_common_types.h"
+#include "vp9/common/vp9_common_types.h"
 
 /* Only need this for fixed-size arrays, for structs just assign. */
 
diff --git a/vp9/common/vp9_context.c b/vp9/common/vp9_context.c
index 90a1f796f..271b45541 100644
--- a/vp9/common/vp9_context.c
+++ b/vp9/common/vp9_context.c
@@ -9,7 +9,7 @@
  */
 
 
-#include "vp9_entropy.h"
+#include "vp9/common/vp9_entropy.h"
 
 /* *** GENERATED FILE: DO NOT EDIT *** */
 
diff --git a/vp9/common/vp9_debugmodes.c b/vp9/common/vp9_debugmodes.c
index 058abb57e..76318d2e1 100644
--- a/vp9/common/vp9_debugmodes.c
+++ b/vp9/common/vp9_debugmodes.c
@@ -9,7 +9,7 @@
  */
 
 #include <stdio.h>
-#include "vp9_blockd.h"
+#include "vp9/common/vp9_blockd.h"
 
 void vp9_print_modes_and_motion_vectors(MODE_INFO *mi, int rows, int cols,
                                         int frame) {
diff --git a/vp9/common/vp9_entropy.c b/vp9/common/vp9_entropy.c
index e6ee2729e..4832b4e9c 100644
--- a/vp9/common/vp9_entropy.c
+++ b/vp9/common/vp9_entropy.c
@@ -11,11 +11,11 @@
 
 #include <stdio.h>
 
-#include "vp9_entropy.h"
+#include "vp9/common/vp9_entropy.h"
 #include "string.h"
-#include "vp9_blockd.h"
-#include "vp9_onyxc_int.h"
-#include "vp9_entropymode.h"
+#include "vp9/common/vp9_blockd.h"
+#include "vp9/common/vp9_onyxc_int.h"
+#include "vp9/common/vp9_entropymode.h"
 #include "vpx_mem/vpx_mem.h"
 
 #define uchar unsigned char     /* typedefs can clash */
@@ -26,7 +26,7 @@ typedef const uint cuint;
 
 typedef vp9_prob Prob;
 
-#include "vp9_coefupdateprobs.h"
+#include "vp9/common/vp9_coefupdateprobs.h"
 
 const int vp9_i8x8_block[4] = {0, 2, 8, 10};
 
@@ -200,7 +200,7 @@ vp9_extra_bit_struct vp9_extra_bits[12] = {
   { 0, 0, 0, 0}
 };
 
-#include "vp9_default_coef_probs.h"
+#include "vp9/common/vp9_default_coef_probs.h"
 
 void vp9_default_coef_probs(VP9_COMMON *pc) {
   vpx_memcpy(pc->fc.coef_probs, default_coef_probs,
diff --git a/vp9/common/vp9_entropy.h b/vp9/common/vp9_entropy.h
index a2053609b..ccf68a422 100644
--- a/vp9/common/vp9_entropy.h
+++ b/vp9/common/vp9_entropy.h
@@ -12,10 +12,10 @@
 #ifndef __INC_ENTROPY_H
 #define __INC_ENTROPY_H
 
-#include "vp9_treecoder.h"
-#include "vp9_blockd.h"
-#include "vp9_common.h"
-#include "vp9_coefupdateprobs.h"
+#include "vp9/common/vp9_treecoder.h"
+#include "vp9/common/vp9_blockd.h"
+#include "vp9/common/vp9_common.h"
+#include "vp9/common/vp9_coefupdateprobs.h"
 
 extern const int vp9_i8x8_block[4];
 
diff --git a/vp9/common/vp9_entropymode.c b/vp9/common/vp9_entropymode.c
index 0eb21ca82..9b48dc97a 100644
--- a/vp9/common/vp9_entropymode.c
+++ b/vp9/common/vp9_entropymode.c
@@ -9,8 +9,8 @@
  */
 
 
-#include "vp9_onyxc_int.h"
-#include "vp9_modecont.h"
+#include "vp9/common/vp9_onyxc_int.h"
+#include "vp9/common/vp9_modecont.h"
 #include "vpx_mem/vpx_mem.h"
 
 
diff --git a/vp9/common/vp9_entropymode.h b/vp9/common/vp9_entropymode.h
index aee6e6c76..0b14cf67e 100644
--- a/vp9/common/vp9_entropymode.h
+++ b/vp9/common/vp9_entropymode.h
@@ -12,8 +12,8 @@
 #ifndef __INC_ENTROPYMODE_H
 #define __INC_ENTROPYMODE_H
 
-#include "vp9_blockd.h"
-#include "vp9_treecoder.h"
+#include "vp9/common/vp9_blockd.h"
+#include "vp9/common/vp9_treecoder.h"
 
 #define SUBMVREF_COUNT 5
 #define VP9_NUMMBSPLITS 4
diff --git a/vp9/common/vp9_entropymv.c b/vp9/common/vp9_entropymv.c
index 8d2ebebc4..94543c54d 100644
--- a/vp9/common/vp9_entropymv.c
+++ b/vp9/common/vp9_entropymv.c
@@ -9,8 +9,8 @@
  */
 
 
-#include "vp9_onyxc_int.h"
-#include "vp9_entropymv.h"
+#include "vp9/common/vp9_onyxc_int.h"
+#include "vp9/common/vp9_entropymv.h"
 
 //#define MV_COUNT_TESTING
 
diff --git a/vp9/common/vp9_entropymv.h b/vp9/common/vp9_entropymv.h
index 3be95117c..b6b35df04 100644
--- a/vp9/common/vp9_entropymv.h
+++ b/vp9/common/vp9_entropymv.h
@@ -12,9 +12,9 @@
 #ifndef __INC_ENTROPYMV_H
 #define __INC_ENTROPYMV_H
 
-#include "vp9_treecoder.h"
+#include "vp9/common/vp9_treecoder.h"
 #include "vpx_config.h"
-#include "vp9_blockd.h"
+#include "vp9/common/vp9_blockd.h"
 
 struct VP9Common;
 
diff --git a/vp9/common/vp9_extend.c b/vp9/common/vp9_extend.c
index 4f2aa0e0c..61c7abfc7 100644
--- a/vp9/common/vp9_extend.c
+++ b/vp9/common/vp9_extend.c
@@ -8,7 +8,7 @@
  *  be found in the AUTHORS file in the root of the source tree.
  */
 
-#include "vp9_extend.h"
+#include "vp9/common/vp9_extend.h"
 #include "vpx_mem/vpx_mem.h"
 
 static void copy_and_extend_plane(unsigned char *s, /* source */
diff --git a/vp9/common/vp9_filter.c b/vp9/common/vp9_filter.c
index 8d5eb9333..18217e627 100644
--- a/vp9/common/vp9_filter.c
+++ b/vp9/common/vp9_filter.c
@@ -10,7 +10,7 @@
 
 
 #include <stdlib.h>
-#include "vp9_filter.h"
+#include "vp9/common/vp9_filter.h"
 #include "vpx_ports/mem.h"
 #include "vp9_rtcd.h"
 
diff --git a/vp9/common/vp9_findnearmv.c b/vp9/common/vp9_findnearmv.c
index bfbac4e18..ed8a99af2 100644
--- a/vp9/common/vp9_findnearmv.c
+++ b/vp9/common/vp9_findnearmv.c
@@ -9,7 +9,7 @@
  */
 
 
-#include "vp9_findnearmv.h"
+#include "vp9/common/vp9_findnearmv.h"
 #include "vp9/common/vp9_sadmxn.h"
 #include "vp9/common/vp9_subpelvar.h"
 #include <limits.h>
diff --git a/vp9/common/vp9_findnearmv.h b/vp9/common/vp9_findnearmv.h
index 759bdbaff..a12a72201 100644
--- a/vp9/common/vp9_findnearmv.h
+++ b/vp9/common/vp9_findnearmv.h
@@ -12,10 +12,10 @@
 #ifndef __INC_FINDNEARMV_H
 #define __INC_FINDNEARMV_H
 
-#include "vp9_mv.h"
-#include "vp9_blockd.h"
-#include "vp9_treecoder.h"
-#include "vp9_onyxc_int.h"
+#include "vp9/common/vp9_mv.h"
+#include "vp9/common/vp9_blockd.h"
+#include "vp9/common/vp9_treecoder.h"
+#include "vp9/common/vp9_onyxc_int.h"
 
 /* check a list of motion vectors by sad score using a number rows of pixels
  * above and a number cols of pixels in the left to select the one with best
diff --git a/vp9/common/vp9_invtrans.c b/vp9/common/vp9_invtrans.c
index 76eb10307..b79977385 100644
--- a/vp9/common/vp9_invtrans.c
+++ b/vp9/common/vp9_invtrans.c
@@ -8,7 +8,7 @@
  *  be found in the AUTHORS file in the root of the source tree.
  */
 
-#include "vp9_invtrans.h"
+#include "vp9/common/vp9_invtrans.h"
 #include "./vp9_rtcd.h"
 
 static void recon_dcblock(MACROBLOCKD *xd) {
diff --git a/vp9/common/vp9_invtrans.h b/vp9/common/vp9_invtrans.h
index 0e50c45d7..9ac9bb1cd 100644
--- a/vp9/common/vp9_invtrans.h
+++ b/vp9/common/vp9_invtrans.h
@@ -12,7 +12,7 @@
 #define __INC_INVTRANS_H
 
 #include "vpx_ports/config.h"
-#include "vp9_blockd.h"
+#include "vp9/common/vp9_blockd.h"
 
 extern void vp9_inverse_transform_b_4x4(MACROBLOCKD *xd, int block, int pitch);
 
diff --git a/vp9/common/vp9_loopfilter.c b/vp9/common/vp9_loopfilter.c
index 73b343974..8d4d014ba 100644
--- a/vp9/common/vp9_loopfilter.c
+++ b/vp9/common/vp9_loopfilter.c
@@ -9,8 +9,8 @@
  */
 
 #include "vpx_config.h"
-#include "vp9_loopfilter.h"
-#include "vp9_onyxc_int.h"
+#include "vp9/common/vp9_loopfilter.h"
+#include "vp9/common/vp9_onyxc_int.h"
 #include "vpx_mem/vpx_mem.h"
 
 #include "vp9/common/vp9_seg_common.h"
diff --git a/vp9/common/vp9_loopfilter.h b/vp9/common/vp9_loopfilter.h
index b3254f692..34d1cd37f 100644
--- a/vp9/common/vp9_loopfilter.h
+++ b/vp9/common/vp9_loopfilter.h
@@ -13,7 +13,7 @@
 
 #include "vpx_ports/mem.h"
 #include "vpx_config.h"
-#include "vp9_blockd.h"
+#include "vp9/common/vp9_blockd.h"
 
 #define MAX_LOOP_FILTER 63
 
diff --git a/vp9/common/vp9_loopfilter_filters.c b/vp9/common/vp9_loopfilter_filters.c
index 9fd6c5fa6..b8cfb9c1a 100644
--- a/vp9/common/vp9_loopfilter_filters.c
+++ b/vp9/common/vp9_loopfilter_filters.c
@@ -10,8 +10,8 @@
 
 #include <stdlib.h>
 #include "vpx_config.h"
-#include "vp9_loopfilter.h"
-#include "vp9_onyxc_int.h"
+#include "vp9/common/vp9_loopfilter.h"
+#include "vp9/common/vp9_onyxc_int.h"
 
 typedef unsigned char uc;
 
diff --git a/vp9/common/vp9_mbpitch.c b/vp9/common/vp9_mbpitch.c
index b42db987a..84e473bb1 100644
--- a/vp9/common/vp9_mbpitch.c
+++ b/vp9/common/vp9_mbpitch.c
@@ -9,7 +9,7 @@
  */
 
 
-#include "vp9_blockd.h"
+#include "vp9/common/vp9_blockd.h"
 
 typedef enum {
   PRED = 0,
diff --git a/vp9/common/vp9_modecont.c b/vp9/common/vp9_modecont.c
index 2f5bbd2ba..64ff377c3 100644
--- a/vp9/common/vp9_modecont.c
+++ b/vp9/common/vp9_modecont.c
@@ -9,7 +9,7 @@
  */
 
 
-#include "vp9_entropy.h"
+#include "vp9/common/vp9_entropy.h"
 
 const int vp9_default_mode_contexts[INTER_MODE_CONTEXTS][4] = {
   {223,     1,     1,    237},  // 0,0 best: Only candidate
diff --git a/vp9/common/vp9_modecontext.c b/vp9/common/vp9_modecontext.c
index e18cf63c1..ab91c0b14 100644
--- a/vp9/common/vp9_modecontext.c
+++ b/vp9/common/vp9_modecontext.c
@@ -9,7 +9,7 @@
  */
 
 
-#include "vp9_entropymode.h"
+#include "vp9/common/vp9_entropymode.h"
 
 const unsigned int vp9_kf_default_bmode_counts[VP9_KF_BINTRAMODES]
                                               [VP9_KF_BINTRAMODES]
diff --git a/vp9/common/vp9_mvref_common.c b/vp9/common/vp9_mvref_common.c
index 33dc3fa5b..dce49304d 100644
--- a/vp9/common/vp9_mvref_common.c
+++ b/vp9/common/vp9_mvref_common.c
@@ -8,7 +8,7 @@
  *  be found in the AUTHORS file in the root of the source tree.
  */
 
-#include "vp9_mvref_common.h"
+#include "vp9/common/vp9_mvref_common.h"
 
 #define MVREF_NEIGHBOURS 8
 static int mb_mv_ref_search[MVREF_NEIGHBOURS][2] = {
diff --git a/vp9/common/vp9_mvref_common.h b/vp9/common/vp9_mvref_common.h
index 9a1877919..eb8626ed2 100644
--- a/vp9/common/vp9_mvref_common.h
+++ b/vp9/common/vp9_mvref_common.h
@@ -8,8 +8,8 @@
  *  be found in the AUTHORS file in the root of the source tree.
  */
 
-#include "vp9_onyxc_int.h"
-#include "vp9_blockd.h"
+#include "vp9/common/vp9_onyxc_int.h"
+#include "vp9/common/vp9_blockd.h"
 
 
 #ifndef __INC_MVREF_COMMON_H
diff --git a/vp9/common/vp9_onyx.h b/vp9/common/vp9_onyx.h
index 92ec667e7..96c7123b4 100644
--- a/vp9/common/vp9_onyx.h
+++ b/vp9/common/vp9_onyx.h
@@ -20,8 +20,8 @@ extern "C"
 #include "vpx/internal/vpx_codec_internal.h"
 #include "vpx/vp8cx.h"
 #include "vpx_scale/yv12config.h"
-#include "vp9_type_aliases.h"
-#include "vp9_ppflags.h"
+#include "vp9/common/vp9_type_aliases.h"
+#include "vp9/common/vp9_ppflags.h"
   typedef int *VP9_PTR;
 
   /* Create/destroy static data structures. */
diff --git a/vp9/common/vp9_onyxc_int.h b/vp9/common/vp9_onyxc_int.h
index bef4b41ac..1bbdaeeb5 100644
--- a/vp9/common/vp9_onyxc_int.h
+++ b/vp9/common/vp9_onyxc_int.h
@@ -15,16 +15,16 @@
 #include "vpx_config.h"
 #include "vpx/internal/vpx_codec_internal.h"
 #include "vp9_rtcd.h"
-#include "vp9_loopfilter.h"
-#include "vp9_entropymv.h"
-#include "vp9_entropy.h"
-#include "vp9_entropymode.h"
+#include "vp9/common/vp9_loopfilter.h"
+#include "vp9/common/vp9_entropymv.h"
+#include "vp9/common/vp9_entropy.h"
+#include "vp9/common/vp9_entropymode.h"
 #if CONFIG_POSTPROC
-#include "vp9_postproc.h"
+#include "vp9/common/vp9_postproc.h"
 #endif
 
 /*#ifdef PACKET_TESTING*/
-#include "vp9_header.h"
+#include "vp9/common/vp9_header.h"
 /*#endif*/
 
 /* Create/destroy static data structures. */
diff --git a/vp9/common/vp9_onyxd.h b/vp9/common/vp9_onyxd.h
index 2fc51db96..af16ee71c 100644
--- a/vp9/common/vp9_onyxd.h
+++ b/vp9/common/vp9_onyxd.h
@@ -18,9 +18,9 @@
 extern "C"
 {
 #endif
-#include "vp9_type_aliases.h"
+#include "vp9/common/vp9_type_aliases.h"
 #include "vpx_scale/yv12config.h"
-#include "vp9_ppflags.h"
+#include "vp9/common/vp9_ppflags.h"
 #include "vpx_ports/mem.h"
 #include "vpx/vpx_codec.h"
 
diff --git a/vp9/common/vp9_postproc.c b/vp9/common/vp9_postproc.c
index aa8186be2..2cf3b6f77 100644
--- a/vp9/common/vp9_postproc.c
+++ b/vp9/common/vp9_postproc.c
@@ -11,10 +11,10 @@
 
 #include "vpx_ports/config.h"
 #include "vpx_scale/yv12config.h"
-#include "vp9_postproc.h"
+#include "vp9/common/vp9_postproc.h"
 #include "vp9/common/vp9_textblit.h"
 #include "vpx_scale/vpxscale.h"
-#include "vp9_systemdependent.h"
+#include "vp9/common/vp9_systemdependent.h"
 #include "./vp9_rtcd.h"
 
 
diff --git a/vp9/common/vp9_postproc.h b/vp9/common/vp9_postproc.h
index de011b575..d7fc30db4 100644
--- a/vp9/common/vp9_postproc.h
+++ b/vp9/common/vp9_postproc.h
@@ -21,8 +21,8 @@ struct postproc_state {
   DECLARE_ALIGNED(16, char, whiteclamp[16]);
   DECLARE_ALIGNED(16, char, bothclamp[16]);
 };
-#include "vp9_onyxc_int.h"
-#include "vp9_ppflags.h"
+#include "vp9/common/vp9_onyxc_int.h"
+#include "vp9/common/vp9_ppflags.h"
 int vp9_post_proc_frame(struct VP9Common *oci, YV12_BUFFER_CONFIG *dest,
                         vp9_ppflags_t *flags);
 
diff --git a/vp9/common/vp9_pred_common.h b/vp9/common/vp9_pred_common.h
index 2628bb3ca..28511c2f2 100644
--- a/vp9/common/vp9_pred_common.h
+++ b/vp9/common/vp9_pred_common.h
@@ -8,8 +8,8 @@
  *  be found in the AUTHORS file in the root of the source tree.
  */
 
-#include "vp9_type_aliases.h"
-#include "vp9_onyxc_int.h"
+#include "vp9/common/vp9_type_aliases.h"
+#include "vp9/common/vp9_onyxc_int.h"
 #include "vp9/common/vp9_blockd.h"
 
 #ifndef __INC_PRED_COMMON_H__
diff --git a/vp9/common/vp9_quant_common.c b/vp9/common/vp9_quant_common.c
index 5d1f2594a..119038121 100644
--- a/vp9/common/vp9_quant_common.c
+++ b/vp9/common/vp9_quant_common.c
@@ -9,7 +9,7 @@
  */
 
 
-#include "vp9_quant_common.h"
+#include "vp9/common/vp9_quant_common.h"
 
 static int dc_qlookup[QINDEX_RANGE];
 static int ac_qlookup[QINDEX_RANGE];
diff --git a/vp9/common/vp9_quant_common.h b/vp9/common/vp9_quant_common.h
index 88588d5d2..6e0555e09 100644
--- a/vp9/common/vp9_quant_common.h
+++ b/vp9/common/vp9_quant_common.h
@@ -10,8 +10,8 @@
 
 
 #include "string.h"
-#include "vp9_blockd.h"
-#include "vp9_onyxc_int.h"
+#include "vp9/common/vp9_blockd.h"
+#include "vp9/common/vp9_onyxc_int.h"
 
 extern void vp9_init_quant_tables();
 extern int vp9_ac_yquant(int QIndex);
diff --git a/vp9/common/vp9_recon.c b/vp9/common/vp9_recon.c
index 9c9029f2a..1f8dfce34 100644
--- a/vp9/common/vp9_recon.c
+++ b/vp9/common/vp9_recon.c
@@ -11,7 +11,7 @@
 
 #include "vpx_ports/config.h"
 #include "vp9_rtcd.h"
-#include "vp9_blockd.h"
+#include "vp9/common/vp9_blockd.h"
 
 void vp9_recon_b_c
 (
diff --git a/vp9/common/vp9_reconinter.c b/vp9/common/vp9_reconinter.c
index eac07ae19..bcd75ec8b 100644
--- a/vp9/common/vp9_reconinter.c
+++ b/vp9/common/vp9_reconinter.c
@@ -11,11 +11,11 @@
 
 #include "vpx_ports/config.h"
 #include "vpx/vpx_integer.h"
-#include "vp9_blockd.h"
-#include "vp9_reconinter.h"
+#include "vp9/common/vp9_blockd.h"
+#include "vp9/common/vp9_reconinter.h"
 #include "vp9/common/vp9_reconintra.h"
 #if CONFIG_RUNTIME_CPU_DETECT
-#include "vp9_onyxc_int.h"
+#include "vp9/common/vp9_onyxc_int.h"
 #endif
 
 void vp9_setup_interp_filters(MACROBLOCKD *xd,
diff --git a/vp9/common/vp9_reconinter.h b/vp9/common/vp9_reconinter.h
index 25a8adc3b..70ffd3bd1 100644
--- a/vp9/common/vp9_reconinter.h
+++ b/vp9/common/vp9_reconinter.h
@@ -11,7 +11,7 @@
 #ifndef __INC_RECONINTER_H
 #define __INC_RECONINTER_H
 
-#include "vp9_onyxc_int.h"
+#include "vp9/common/vp9_onyxc_int.h"
 
 extern void vp9_build_1st_inter16x16_predictors_mby(MACROBLOCKD *xd,
                                                     unsigned char *dst_y,
diff --git a/vp9/common/vp9_reconintra.c b/vp9/common/vp9_reconintra.c
index 8199b94ae..5c5d4abbb 100644
--- a/vp9/common/vp9_reconintra.c
+++ b/vp9/common/vp9_reconintra.c
@@ -11,7 +11,7 @@
 #include <stdio.h>
 #include "vpx_ports/config.h"
 #include "vp9_rtcd.h"
-#include "vp9_reconintra.h"
+#include "vp9/common/vp9_reconintra.h"
 #include "vpx_mem/vpx_mem.h"
 
 /* For skip_recon_mb(), add vp9_build_intra_predictors_mby_s(MACROBLOCKD *xd)
diff --git a/vp9/common/vp9_reconintra.h b/vp9/common/vp9_reconintra.h
index dd35b06ad..3ef44c85d 100644
--- a/vp9/common/vp9_reconintra.h
+++ b/vp9/common/vp9_reconintra.h
@@ -11,7 +11,7 @@
 #ifndef __INC_RECONINTRA_H
 #define __INC_RECONINTRA_H
 
-#include "vp9_blockd.h"
+#include "vp9/common/vp9_blockd.h"
 
 extern void vp9_recon_intra_mbuv(MACROBLOCKD *xd);
 extern B_PREDICTION_MODE vp9_find_dominant_direction(unsigned char *ptr,
diff --git a/vp9/common/vp9_reconintra4x4.c b/vp9/common/vp9_reconintra4x4.c
index d5203acd0..e4a24f2cb 100644
--- a/vp9/common/vp9_reconintra4x4.c
+++ b/vp9/common/vp9_reconintra4x4.c
@@ -11,7 +11,7 @@
 
 #include "vpx_ports/config.h"
 #include "vpx_mem/vpx_mem.h"
-#include "vp9_reconintra.h"
+#include "vp9/common/vp9_reconintra.h"
 #include "vp9_rtcd.h"
 
 #if CONFIG_NEWBINTRAMODES
diff --git a/vp9/common/vp9_seg_common.h b/vp9/common/vp9_seg_common.h
index 20959a705..29eee4ce9 100644
--- a/vp9/common/vp9_seg_common.h
+++ b/vp9/common/vp9_seg_common.h
@@ -8,8 +8,8 @@
  *  be found in the AUTHORS file in the root of the source tree.
  */
 
-#include "vp9_type_aliases.h"
-#include "vp9_onyxc_int.h"
+#include "vp9/common/vp9_type_aliases.h"
+#include "vp9/common/vp9_onyxc_int.h"
 #include "vp9/common/vp9_blockd.h"
 
 #ifndef __INC_SEG_COMMON_H__
diff --git a/vp9/common/vp9_setupintrarecon.c b/vp9/common/vp9_setupintrarecon.c
index 3fe4e3e50..2c84cd0c4 100644
--- a/vp9/common/vp9_setupintrarecon.c
+++ b/vp9/common/vp9_setupintrarecon.c
@@ -9,7 +9,7 @@
  */
 
 
-#include "vp9_setupintrarecon.h"
+#include "vp9/common/vp9_setupintrarecon.h"
 #include "vpx_mem/vpx_mem.h"
 
 void vp9_setup_intra_recon(YV12_BUFFER_CONFIG *ybf) {
diff --git a/vp9/common/vp9_swapyv12buffer.c b/vp9/common/vp9_swapyv12buffer.c
index 7882e0be0..b01462538 100644
--- a/vp9/common/vp9_swapyv12buffer.c
+++ b/vp9/common/vp9_swapyv12buffer.c
@@ -8,7 +8,7 @@
  *  be found in the AUTHORS file in the root of the source tree.
  */
 
-#include "vp9_swapyv12buffer.h"
+#include "vp9/common/vp9_swapyv12buffer.h"
 
 void vp9_swap_yv12_buffer(YV12_BUFFER_CONFIG *new_frame,
                           YV12_BUFFER_CONFIG *last_frame) {
diff --git a/vp9/common/vp9_treecoder.c b/vp9/common/vp9_treecoder.c
index 096dd59e5..64018a100 100644
--- a/vp9/common/vp9_treecoder.c
+++ b/vp9/common/vp9_treecoder.c
@@ -16,7 +16,7 @@
 #endif
 #include <stdio.h>
 
-#include "vp9_treecoder.h"
+#include "vp9/common/vp9_treecoder.h"
 
 static void tree2tok(
   struct vp9_token_struct *const p,
diff --git a/vp9/decoder/vp9_asm_dec_offsets.c b/vp9/decoder/vp9_asm_dec_offsets.c
index ece315ac8..5abc40f8c 100644
--- a/vp9/decoder/vp9_asm_dec_offsets.c
+++ b/vp9/decoder/vp9_asm_dec_offsets.c
@@ -10,7 +10,7 @@
 
 
 #include "vpx_ports/asm_offsets.h"
-#include "vp9_onyxd_int.h"
+#include "vp9/decoder/vp9_onyxd_int.h"
 
 BEGIN
 
diff --git a/vp9/decoder/vp9_dboolhuff.c b/vp9/decoder/vp9_dboolhuff.c
index 885ec0df6..5f1ef0408 100644
--- a/vp9/decoder/vp9_dboolhuff.c
+++ b/vp9/decoder/vp9_dboolhuff.c
@@ -9,7 +9,7 @@
  */
 
 
-#include "vp9_dboolhuff.h"
+#include "vp9/decoder/vp9_dboolhuff.h"
 #include "vpx_ports/mem.h"
 #include "vpx_mem/vpx_mem.h"
 
diff --git a/vp9/decoder/vp9_decodemv.c b/vp9/decoder/vp9_decodemv.c
index f17e526ba..6842a150d 100644
--- a/vp9/decoder/vp9_decodemv.c
+++ b/vp9/decoder/vp9_decodemv.c
@@ -9,10 +9,10 @@
  */
 
 
-#include "vp9_treereader.h"
+#include "vp9/decoder/vp9_treereader.h"
 #include "vp9/common/vp9_entropymv.h"
 #include "vp9/common/vp9_entropymode.h"
-#include "vp9_onyxd_int.h"
+#include "vp9/decoder/vp9_onyxd_int.h"
 #include "vp9/common/vp9_findnearmv.h"
 
 #include "vp9/common/vp9_seg_common.h"
diff --git a/vp9/decoder/vp9_decodemv.h b/vp9/decoder/vp9_decodemv.h
index 10ae4f54e..a5c44670c 100644
--- a/vp9/decoder/vp9_decodemv.h
+++ b/vp9/decoder/vp9_decodemv.h
@@ -9,7 +9,7 @@
  */
 
 
-#include "vp9_onyxd_int.h"
+#include "vp9/decoder/vp9_onyxd_int.h"
 
 void vp9_decode_mb_mode_mv(VP9D_COMP* const pbi,
                            MACROBLOCKD* const xd,
diff --git a/vp9/decoder/vp9_decodframe.c b/vp9/decoder/vp9_decodframe.c
index 2adbb903b..d253f30ba 100644
--- a/vp9/decoder/vp9_decodframe.c
+++ b/vp9/decoder/vp9_decodframe.c
@@ -9,13 +9,13 @@
  */
 
 
-#include "vp9_onyxd_int.h"
+#include "vp9/decoder/vp9_onyxd_int.h"
 #include "vp9/common/vp9_header.h"
 #include "vp9/common/vp9_reconintra.h"
 #include "vp9/common/vp9_reconintra4x4.h"
 #include "vp9/common/vp9_reconinter.h"
 #include "vp9/decoder/vp9_decodframe.h"
-#include "vp9_detokenize.h"
+#include "vp9/decoder/vp9_detokenize.h"
 #include "vp9/common/vp9_invtrans.h"
 #include "vp9/common/vp9_alloccommon.h"
 #include "vp9/common/vp9_entropymode.h"
@@ -23,11 +23,11 @@
 #include "vpx_scale/vpxscale.h"
 #include "vp9/common/vp9_setupintrarecon.h"
 
-#include "vp9_decodemv.h"
+#include "vp9/decoder/vp9_decodemv.h"
 #include "vp9/common/vp9_extend.h"
 #include "vp9/common/vp9_modecont.h"
 #include "vpx_mem/vpx_mem.h"
-#include "vp9_dboolhuff.h"
+#include "vp9/decoder/vp9_dboolhuff.h"
 
 #include "vp9/common/vp9_seg_common.h"
 #include "vp9/common/vp9_entropy.h"
diff --git a/vp9/decoder/vp9_dequantize.c b/vp9/decoder/vp9_dequantize.c
index f3a22b543..633e3a4bf 100644
--- a/vp9/decoder/vp9_dequantize.c
+++ b/vp9/decoder/vp9_dequantize.c
@@ -10,9 +10,9 @@
 
 
 #include "vp9_rtcd.h"
-#include "vp9_dequantize.h"
+#include "vp9/decoder/vp9_dequantize.h"
 #include "vpx_mem/vpx_mem.h"
-#include "vp9_onyxd_int.h"
+#include "vp9/decoder/vp9_onyxd_int.h"
 
 #ifdef DEC_DEBUG
 extern int dec_debug;
diff --git a/vp9/decoder/vp9_detokenize.c b/vp9/decoder/vp9_detokenize.c
index c55e3620a..1a7a08fa4 100644
--- a/vp9/decoder/vp9_detokenize.c
+++ b/vp9/decoder/vp9_detokenize.c
@@ -11,10 +11,10 @@
 
 #include "vp9/common/vp9_type_aliases.h"
 #include "vp9/common/vp9_blockd.h"
-#include "vp9_onyxd_int.h"
+#include "vp9/decoder/vp9_onyxd_int.h"
 #include "vpx_mem/vpx_mem.h"
 #include "vpx_ports/mem.h"
-#include "vp9_detokenize.h"
+#include "vp9/decoder/vp9_detokenize.h"
 
 #include "vp9/common/vp9_seg_common.h"
 
diff --git a/vp9/decoder/vp9_detokenize.h b/vp9/decoder/vp9_detokenize.h
index 1425a36e3..e1a3b44f3 100644
--- a/vp9/decoder/vp9_detokenize.h
+++ b/vp9/decoder/vp9_detokenize.h
@@ -12,7 +12,7 @@
 #ifndef DETOKENIZE_H
 #define DETOKENIZE_H
 
-#include "vp9_onyxd_int.h"
+#include "vp9/decoder/vp9_onyxd_int.h"
 
 void vp9_reset_mb_tokens_context(MACROBLOCKD* const);
 
diff --git a/vp9/decoder/vp9_onyxd_if.c b/vp9/decoder/vp9_onyxd_if.c
index 70671683b..e92712bd6 100644
--- a/vp9/decoder/vp9_onyxd_if.c
+++ b/vp9/decoder/vp9_onyxd_if.c
@@ -14,7 +14,7 @@
 #include "vp9/common/vp9_postproc.h"
 #endif
 #include "vp9/common/vp9_onyxd.h"
-#include "vp9_onyxd_int.h"
+#include "vp9/decoder/vp9_onyxd_int.h"
 #include "vpx_mem/vpx_mem.h"
 #include "vp9/common/vp9_alloccommon.h"
 #include "vp9/common/vp9_loopfilter.h"
@@ -27,7 +27,7 @@
 #include "vp9/common/vp9_systemdependent.h"
 #include "vpx_ports/vpx_timer.h"
 #include "vp9/decoder/vp9_decodframe.h"
-#include "vp9_detokenize.h"
+#include "vp9/decoder/vp9_detokenize.h"
 #if ARCH_ARM
 #include "vpx_ports/arm.h"
 #endif
diff --git a/vp9/decoder/vp9_onyxd_int.h b/vp9/decoder/vp9_onyxd_int.h
index 023e8eefd..603455af0 100644
--- a/vp9/decoder/vp9_onyxd_int.h
+++ b/vp9/decoder/vp9_onyxd_int.h
@@ -13,9 +13,9 @@
 #define __INC_ONYXD_INT_H
 #include "vpx_ports/config.h"
 #include "vp9/common/vp9_onyxd.h"
-#include "vp9_treereader.h"
+#include "vp9/decoder/vp9_treereader.h"
 #include "vp9/common/vp9_onyxc_int.h"
-#include "vp9_dequantize.h"
+#include "vp9/decoder/vp9_dequantize.h"
 
 // #define DEC_DEBUG
 
diff --git a/vp9/decoder/vp9_treereader.h b/vp9/decoder/vp9_treereader.h
index 4c49c9a75..ac1293cc7 100644
--- a/vp9/decoder/vp9_treereader.h
+++ b/vp9/decoder/vp9_treereader.h
@@ -14,7 +14,7 @@
 
 #include "vp9/common/vp9_treecoder.h"
 
-#include "vp9_dboolhuff.h"
+#include "vp9/decoder/vp9_dboolhuff.h"
 
 typedef BOOL_DECODER vp9_reader;
 
diff --git a/vp9/encoder/vp9_asm_enc_offsets.c b/vp9/encoder/vp9_asm_enc_offsets.c
index 52b7e9d01..3fe9c8fb7 100644
--- a/vp9/encoder/vp9_asm_enc_offsets.c
+++ b/vp9/encoder/vp9_asm_enc_offsets.c
@@ -11,11 +11,11 @@
 
 #include "vpx_ports/asm_offsets.h"
 #include "vpx_config.h"
-#include "vp9_block.h"
+#include "vp9/encoder/vp9_block.h"
 #include "vp9/common/vp9_blockd.h"
-#include "vp9_onyx_int.h"
-#include "vp9_treewriter.h"
-#include "vp9_tokenize.h"
+#include "vp9/encoder/vp9_onyx_int.h"
+#include "vp9/encoder/vp9_treewriter.h"
+#include "vp9/encoder/vp9_tokenize.h"
 
 BEGIN
 
diff --git a/vp9/encoder/vp9_bitstream.c b/vp9/encoder/vp9_bitstream.c
index 73c116766..644f2082b 100644
--- a/vp9/encoder/vp9_bitstream.c
+++ b/vp9/encoder/vp9_bitstream.c
@@ -10,10 +10,10 @@
 
 
 #include "vp9/common/vp9_header.h"
-#include "vp9_encodemv.h"
+#include "vp9/encoder/vp9_encodemv.h"
 #include "vp9/common/vp9_entropymode.h"
 #include "vp9/common/vp9_findnearmv.h"
-#include "vp9_mcomp.h"
+#include "vp9/encoder/vp9_mcomp.h"
 #include "vp9/common/vp9_systemdependent.h"
 #include <assert.h>
 #include <stdio.h>
@@ -21,8 +21,8 @@
 #include "vp9/common/vp9_pragmas.h"
 #include "vpx/vpx_encoder.h"
 #include "vpx_mem/vpx_mem.h"
-#include "vp9_bitstream.h"
-#include "vp9_segmentation.h"
+#include "vp9/encoder/vp9_bitstream.h"
+#include "vp9/encoder/vp9_segmentation.h"
 
 #include "vp9/common/vp9_seg_common.h"
 #include "vp9/common/vp9_pred_common.h"
diff --git a/vp9/encoder/vp9_boolhuff.c b/vp9/encoder/vp9_boolhuff.c
index 2689ab601..d1b1e0e89 100644
--- a/vp9/encoder/vp9_boolhuff.c
+++ b/vp9/encoder/vp9_boolhuff.c
@@ -9,7 +9,7 @@
  */
 
 #include <assert.h>
-#include "vp9_boolhuff.h"
+#include "vp9/encoder/vp9_boolhuff.h"
 
 #if defined(SECTIONBITS_OUTPUT)
 unsigned __int64 Sectionbits[500];
diff --git a/vp9/encoder/vp9_encodeframe.c b/vp9/encoder/vp9_encodeframe.c
index fe486b192..378994630 100644
--- a/vp9/encoder/vp9_encodeframe.c
+++ b/vp9/encoder/vp9_encodeframe.c
@@ -11,20 +11,20 @@
 
 #include "vpx_ports/config.h"
 #include "vp9/encoder/vp9_encodeframe.h"
-#include "vp9_encodemb.h"
-#include "vp9_encodemv.h"
+#include "vp9/encoder/vp9_encodemb.h"
+#include "vp9/encoder/vp9_encodemv.h"
 #include "vp9/common/vp9_common.h"
-#include "vp9_onyx_int.h"
+#include "vp9/encoder/vp9_onyx_int.h"
 #include "vp9/common/vp9_extend.h"
 #include "vp9/common/vp9_entropymode.h"
 #include "vp9/common/vp9_quant_common.h"
-#include "vp9_segmentation.h"
+#include "vp9/encoder/vp9_segmentation.h"
 #include "vp9/common/vp9_setupintrarecon.h"
 #include "vp9/common/vp9_reconintra4x4.h"
-#include "vp9_encodeintra.h"
+#include "vp9/encoder/vp9_encodeintra.h"
 #include "vp9/common/vp9_reconinter.h"
 #include "vp9/common/vp9_invtrans.h"
-#include "vp9_rdopt.h"
+#include "vp9/encoder/vp9_rdopt.h"
 #include "vp9/common/vp9_findnearmv.h"
 #include "vp9/common/vp9_reconintra.h"
 #include "vp9/common/vp9_seg_common.h"
diff --git a/vp9/encoder/vp9_encodeintra.c b/vp9/encoder/vp9_encodeintra.c
index 185b43192..017c178b9 100644
--- a/vp9/encoder/vp9_encodeintra.c
+++ b/vp9/encoder/vp9_encodeintra.c
@@ -10,12 +10,12 @@
 
 #include "vpx_ports/config.h"
 #include "vp9_rtcd.h"
-#include "vp9_quantize.h"
+#include "vp9/encoder/vp9_quantize.h"
 #include "vp9/common/vp9_reconintra.h"
 #include "vp9/common/vp9_reconintra4x4.h"
-#include "vp9_encodemb.h"
+#include "vp9/encoder/vp9_encodemb.h"
 #include "vp9/common/vp9_invtrans.h"
-#include "vp9_encodeintra.h"
+#include "vp9/encoder/vp9_encodeintra.h"
 
 #if CONFIG_RUNTIME_CPU_DETECT
 #define IF_RTCD(x) (x)
diff --git a/vp9/encoder/vp9_encodeintra.h b/vp9/encoder/vp9_encodeintra.h
index 8d6f41e62..363254eb0 100644
--- a/vp9/encoder/vp9_encodeintra.h
+++ b/vp9/encoder/vp9_encodeintra.h
@@ -11,7 +11,7 @@
 #ifndef __ENCODEINTRA_H_
 #define __ENCODEINTRA_H_
 
-#include "vp9_onyx_int.h"
+#include "vp9/encoder/vp9_onyx_int.h"
 
 int vp9_encode_intra(VP9_COMP *cpi, MACROBLOCK *x, int use_16x16_pred);
 void vp9_encode_intra16x16mby(MACROBLOCK *x);
diff --git a/vp9/encoder/vp9_encodemb.c b/vp9/encoder/vp9_encodemb.c
index 145f75a3f..1a7a38261 100644
--- a/vp9/encoder/vp9_encodemb.c
+++ b/vp9/encoder/vp9_encodemb.c
@@ -9,14 +9,14 @@
  */
 
 #include "vpx_ports/config.h"
-#include "vp9_encodemb.h"
+#include "vp9/encoder/vp9_encodemb.h"
 #include "vp9/common/vp9_reconinter.h"
-#include "vp9_quantize.h"
-#include "vp9_tokenize.h"
+#include "vp9/encoder/vp9_quantize.h"
+#include "vp9/encoder/vp9_tokenize.h"
 #include "vp9/common/vp9_invtrans.h"
 #include "vp9/common/vp9_reconintra.h"
 #include "vpx_mem/vpx_mem.h"
-#include "vp9_rdopt.h"
+#include "vp9/encoder/vp9_rdopt.h"
 #include "vp9/common/vp9_systemdependent.h"
 #include "vp9_rtcd.h"
 
diff --git a/vp9/encoder/vp9_encodemb.h b/vp9/encoder/vp9_encodemb.h
index 3857c6648..b56dcece9 100644
--- a/vp9/encoder/vp9_encodemb.h
+++ b/vp9/encoder/vp9_encodemb.h
@@ -13,7 +13,7 @@
 #define __INC_ENCODEMB_H
 
 #include "vpx_ports/config.h"
-#include "vp9_block.h"
+#include "vp9/encoder/vp9_block.h"
 
 typedef struct {
   MB_PREDICTION_MODE mode;
@@ -25,7 +25,7 @@ typedef struct {
 } MODE_DEFINITION;
 
 
-#include "vp9_onyx_int.h"
+#include "vp9/encoder/vp9_onyx_int.h"
 struct VP9_ENCODER_RTCD;
 void vp9_encode_inter16x16(MACROBLOCK *x);
 
diff --git a/vp9/encoder/vp9_encodemv.c b/vp9/encoder/vp9_encodemv.c
index 301fa24b1..b2589c107 100644
--- a/vp9/encoder/vp9_encodemv.c
+++ b/vp9/encoder/vp9_encodemv.c
@@ -10,7 +10,7 @@
 
 
 #include "vp9/common/vp9_common.h"
-#include "vp9_encodemv.h"
+#include "vp9/encoder/vp9_encodemv.h"
 #include "vp9/common/vp9_entropymode.h"
 #include "vp9/common/vp9_systemdependent.h"
 
diff --git a/vp9/encoder/vp9_encodemv.h b/vp9/encoder/vp9_encodemv.h
index f3589c147..ac09bcbdf 100644
--- a/vp9/encoder/vp9_encodemv.h
+++ b/vp9/encoder/vp9_encodemv.h
@@ -12,7 +12,7 @@
 #ifndef __INC_ENCODEMV_H
 #define __INC_ENCODEMV_H
 
-#include "vp9_onyx_int.h"
+#include "vp9/encoder/vp9_onyx_int.h"
 
 void vp9_write_nmv_probs(VP9_COMP* const, int usehp, vp9_writer* const);
 void vp9_encode_nmv(vp9_writer* const w, const MV* const mv,
diff --git a/vp9/encoder/vp9_firstpass.c b/vp9/encoder/vp9_firstpass.c
index 4a8f5ef23..65476f2ed 100644
--- a/vp9/encoder/vp9_firstpass.c
+++ b/vp9/encoder/vp9_firstpass.c
@@ -10,27 +10,27 @@
 
 #include "math.h"
 #include "limits.h"
-#include "vp9_block.h"
-#include "vp9_onyx_int.h"
-#include "vp9_variance.h"
-#include "vp9_encodeintra.h"
+#include "vp9/encoder/vp9_block.h"
+#include "vp9/encoder/vp9_onyx_int.h"
+#include "vp9/encoder/vp9_variance.h"
+#include "vp9/encoder/vp9_encodeintra.h"
 #include "vp9/common/vp9_setupintrarecon.h"
-#include "vp9_mcomp.h"
-#include "vp9_firstpass.h"
+#include "vp9/encoder/vp9_mcomp.h"
+#include "vp9/encoder/vp9_firstpass.h"
 #include "vpx_scale/vpxscale.h"
 #include "vp9/encoder/vp9_encodeframe.h"
-#include "vp9_encodemb.h"
+#include "vp9/encoder/vp9_encodemb.h"
 #include "vp9/common/vp9_extend.h"
 #include "vp9/common/vp9_systemdependent.h"
 #include "vpx_mem/vpx_mem.h"
 #include "vp9/common/vp9_swapyv12buffer.h"
 #include <stdio.h>
 #include "vp9/encoder/vp9_quantize.h"
-#include "vp9_rdopt.h"
-#include "vp9_ratectrl.h"
+#include "vp9/encoder/vp9_rdopt.h"
+#include "vp9/encoder/vp9_ratectrl.h"
 #include "vp9/common/vp9_quant_common.h"
 #include "vp9/common/vp9_entropymv.h"
-#include "vp9_encodemv.h"
+#include "vp9/encoder/vp9_encodemv.h"
 
 #define OUTPUT_FPF 0
 
diff --git a/vp9/encoder/vp9_lookahead.c b/vp9/encoder/vp9_lookahead.c
index ae17656dc..a51c78656 100644
--- a/vp9/encoder/vp9_lookahead.c
+++ b/vp9/encoder/vp9_lookahead.c
@@ -10,7 +10,7 @@
 #include <assert.h>
 #include <stdlib.h>
 #include "vpx_config.h"
-#include "vp9_lookahead.h"
+#include "vp9/encoder/vp9_lookahead.h"
 #include "vp9/common/vp9_extend.h"
 
 #define MAX_LAG_BUFFERS 25
diff --git a/vp9/encoder/vp9_mcomp.c b/vp9/encoder/vp9_mcomp.c
index b9be68c79..04ee3f610 100644
--- a/vp9/encoder/vp9_mcomp.c
+++ b/vp9/encoder/vp9_mcomp.c
@@ -10,7 +10,7 @@
 
 
 #include "vp9/encoder/vp9_onyx_int.h"
-#include "vp9_mcomp.h"
+#include "vp9/encoder/vp9_mcomp.h"
 #include "vpx_mem/vpx_mem.h"
 #include "vpx_ports/config.h"
 #include <stdio.h>
diff --git a/vp9/encoder/vp9_mcomp.h b/vp9/encoder/vp9_mcomp.h
index 41ba3f8c7..81fe70c85 100644
--- a/vp9/encoder/vp9_mcomp.h
+++ b/vp9/encoder/vp9_mcomp.h
@@ -12,8 +12,8 @@
 #ifndef __INC_MCOMP_H
 #define __INC_MCOMP_H
 
-#include "vp9_block.h"
-#include "vp9_variance.h"
+#include "vp9/encoder/vp9_block.h"
+#include "vp9/encoder/vp9_variance.h"
 
 #ifdef ENTROPY_STATS
 extern void init_mv_ref_counts();
diff --git a/vp9/encoder/vp9_modecosts.c b/vp9/encoder/vp9_modecosts.c
index 5c2eeda84..7d9462f94 100644
--- a/vp9/encoder/vp9_modecosts.c
+++ b/vp9/encoder/vp9_modecosts.c
@@ -10,8 +10,8 @@
 
 
 #include "vp9/common/vp9_blockd.h"
-#include "vp9_onyx_int.h"
-#include "vp9_treewriter.h"
+#include "vp9/encoder/vp9_onyx_int.h"
+#include "vp9/encoder/vp9_treewriter.h"
 #include "vp9/common/vp9_entropymode.h"
 
 
diff --git a/vp9/encoder/vp9_onyx_if.c b/vp9/encoder/vp9_onyx_if.c
index 31fc126eb..754096d36 100644
--- a/vp9/encoder/vp9_onyx_if.c
+++ b/vp9/encoder/vp9_onyx_if.c
@@ -11,18 +11,18 @@
 
 #include "vpx_config.h"
 #include "vp9/common/vp9_onyxc_int.h"
-#include "vp9_onyx_int.h"
+#include "vp9/encoder/vp9_onyx_int.h"
 #include "vp9/common/vp9_systemdependent.h"
-#include "vp9_quantize.h"
+#include "vp9/encoder/vp9_quantize.h"
 #include "vp9/common/vp9_alloccommon.h"
-#include "vp9_mcomp.h"
-#include "vp9_firstpass.h"
-#include "vp9_psnr.h"
+#include "vp9/encoder/vp9_mcomp.h"
+#include "vp9/encoder/vp9_firstpass.h"
+#include "vp9/encoder/vp9_psnr.h"
 #include "vpx_scale/vpxscale.h"
 #include "vp9/common/vp9_extend.h"
-#include "vp9_ratectrl.h"
+#include "vp9/encoder/vp9_ratectrl.h"
 #include "vp9/common/vp9_quant_common.h"
-#include "vp9_segmentation.h"
+#include "vp9/encoder/vp9_segmentation.h"
 #include "./vp9_rtcd.h"
 #if CONFIG_POSTPROC
 #include "vp9/common/vp9_postproc.h"
@@ -32,12 +32,11 @@
 #include "vpx_ports/vpx_timer.h"
 
 #include "vp9/common/vp9_seg_common.h"
-#include "vp9_mbgraph.h"
+#include "vp9/encoder/vp9_mbgraph.h"
 #include "vp9/common/vp9_pred_common.h"
 #include "vp9/encoder/vp9_rdopt.h"
-#include "vp9_bitstream.h"
+#include "vp9/encoder/vp9_bitstream.h"
 #include "vp9/encoder/vp9_picklpf.h"
-#include "vp9_ratectrl.h"
 #include "vp9/common/vp9_mvref_common.h"
 
 
diff --git a/vp9/encoder/vp9_onyx_int.h b/vp9/encoder/vp9_onyx_int.h
index 79b35b41e..c71888e29 100644
--- a/vp9/encoder/vp9_onyx_int.h
+++ b/vp9/encoder/vp9_onyx_int.h
@@ -15,19 +15,19 @@
 #include <stdio.h>
 #include "vpx_ports/config.h"
 #include "vp9/common/vp9_onyx.h"
-#include "vp9_treewriter.h"
-#include "vp9_tokenize.h"
+#include "vp9/encoder/vp9_treewriter.h"
+#include "vp9/encoder/vp9_tokenize.h"
 #include "vp9/common/vp9_onyxc_int.h"
-#include "vp9_variance.h"
-#include "vp9_encodemb.h"
-#include "vp9_quantize.h"
+#include "vp9/encoder/vp9_variance.h"
+#include "vp9/encoder/vp9_encodemb.h"
+#include "vp9/encoder/vp9_quantize.h"
 #include "vp9/common/vp9_entropy.h"
 #include "vp9/common/vp9_entropymode.h"
 #include "vpx_ports/mem.h"
 #include "vpx/internal/vpx_codec_internal.h"
-#include "vp9_mcomp.h"
+#include "vp9/encoder/vp9_mcomp.h"
 #include "vp9/common/vp9_findnearmv.h"
-#include "vp9_lookahead.h"
+#include "vp9/encoder/vp9_lookahead.h"
 
 // #define SPEEDSTATS 1
 #define MIN_GF_INTERVAL             4
diff --git a/vp9/encoder/vp9_picklpf.c b/vp9/encoder/vp9_picklpf.c
index 4c971e200..395600ce2 100644
--- a/vp9/encoder/vp9_picklpf.c
+++ b/vp9/encoder/vp9_picklpf.c
@@ -10,9 +10,9 @@
 
 
 #include "vp9/common/vp9_onyxc_int.h"
-#include "vp9_onyx_int.h"
+#include "vp9/encoder/vp9_onyx_int.h"
 #include "vp9/encoder/vp9_picklpf.h"
-#include "vp9_quantize.h"
+#include "vp9/encoder/vp9_quantize.h"
 #include "vpx_mem/vpx_mem.h"
 #include "vpx_scale/vpxscale.h"
 #include "vp9/common/vp9_alloccommon.h"
diff --git a/vp9/encoder/vp9_quantize.c b/vp9/encoder/vp9_quantize.c
index f3c2bcb89..d3cd8eb54 100644
--- a/vp9/encoder/vp9_quantize.c
+++ b/vp9/encoder/vp9_quantize.c
@@ -11,8 +11,8 @@
 #include <math.h>
 #include "vpx_mem/vpx_mem.h"
 
-#include "vp9_onyx_int.h"
-#include "vp9_quantize.h"
+#include "vp9/encoder/vp9_onyx_int.h"
+#include "vp9/encoder/vp9_quantize.h"
 #include "vp9/common/vp9_quant_common.h"
 
 #include "vp9/common/vp9_seg_common.h"
diff --git a/vp9/encoder/vp9_quantize.h b/vp9/encoder/vp9_quantize.h
index a62e7723e..5a0f7e058 100644
--- a/vp9/encoder/vp9_quantize.h
+++ b/vp9/encoder/vp9_quantize.h
@@ -11,7 +11,7 @@
 #ifndef __INC_QUANTIZE_H
 #define __INC_QUANTIZE_H
 
-#include "vp9_block.h"
+#include "vp9/encoder/vp9_block.h"
 
 #define prototype_quantize_block(sym) \
   void (sym)(BLOCK *b,BLOCKD *d)
diff --git a/vp9/encoder/vp9_ratectrl.c b/vp9/encoder/vp9_ratectrl.c
index 0ceb4f653..1d7248547 100644
--- a/vp9/encoder/vp9_ratectrl.c
+++ b/vp9/encoder/vp9_ratectrl.c
@@ -19,11 +19,11 @@
 #include "vp9/common/vp9_alloccommon.h"
 #include "vp9/common/vp9_modecont.h"
 #include "vp9/common/vp9_common.h"
-#include "vp9_ratectrl.h"
+#include "vp9/encoder/vp9_ratectrl.h"
 #include "vp9/common/vp9_entropymode.h"
 #include "vpx_mem/vpx_mem.h"
 #include "vp9/common/vp9_systemdependent.h"
-#include "vp9_encodemv.h"
+#include "vp9/encoder/vp9_encodemv.h"
 #include "vp9/common/vp9_quant_common.h"
 
 #define MIN_BPB_FACTOR          0.005
diff --git a/vp9/encoder/vp9_ratectrl.h b/vp9/encoder/vp9_ratectrl.h
index a64b8f927..9d6960727 100644
--- a/vp9/encoder/vp9_ratectrl.h
+++ b/vp9/encoder/vp9_ratectrl.h
@@ -11,7 +11,7 @@
 
 #if !defined __INC_RATECTRL_H
 
-#include "vp9_onyx_int.h"
+#include "vp9/encoder/vp9_onyx_int.h"
 
 #define FRAME_OVERHEAD_BITS 200
 
diff --git a/vp9/encoder/vp9_rdopt.c b/vp9/encoder/vp9_rdopt.c
index 017bf0377..760593acb 100644
--- a/vp9/encoder/vp9_rdopt.c
+++ b/vp9/encoder/vp9_rdopt.c
@@ -15,23 +15,23 @@
 #include <assert.h>
 #include "vp9/common/vp9_pragmas.h"
 
-#include "vp9_tokenize.h"
-#include "vp9_treewriter.h"
-#include "vp9_onyx_int.h"
-#include "vp9_modecosts.h"
-#include "vp9_encodeintra.h"
+#include "vp9/encoder/vp9_tokenize.h"
+#include "vp9/encoder/vp9_treewriter.h"
+#include "vp9/encoder/vp9_onyx_int.h"
+#include "vp9/encoder/vp9_modecosts.h"
+#include "vp9/encoder/vp9_encodeintra.h"
 #include "vp9/common/vp9_entropymode.h"
 #include "vp9/common/vp9_reconinter.h"
 #include "vp9/common/vp9_reconintra.h"
 #include "vp9/common/vp9_reconintra4x4.h"
 #include "vp9/common/vp9_findnearmv.h"
 #include "vp9/common/vp9_quant_common.h"
-#include "vp9_encodemb.h"
-#include "vp9_quantize.h"
-#include "vp9_variance.h"
-#include "vp9_mcomp.h"
-#include "vp9_rdopt.h"
-#include "vp9_ratectrl.h"
+#include "vp9/encoder/vp9_encodemb.h"
+#include "vp9/encoder/vp9_quantize.h"
+#include "vp9/encoder/vp9_variance.h"
+#include "vp9/encoder/vp9_mcomp.h"
+#include "vp9/encoder/vp9_rdopt.h"
+#include "vp9/encoder/vp9_ratectrl.h"
 #include "vpx_mem/vpx_mem.h"
 #include "vp9/common/vp9_systemdependent.h"
 #include "vp9/encoder/vp9_encodemv.h"
diff --git a/vp9/encoder/vp9_segmentation.c b/vp9/encoder/vp9_segmentation.c
index a9efff9f8..bebfdfa51 100644
--- a/vp9/encoder/vp9_segmentation.c
+++ b/vp9/encoder/vp9_segmentation.c
@@ -11,7 +11,7 @@
 
 #include "limits.h"
 #include "vpx_mem/vpx_mem.h"
-#include "vp9_segmentation.h"
+#include "vp9/encoder/vp9_segmentation.h"
 #include "vp9/common/vp9_pred_common.h"
 
 void vp9_update_gf_useage_maps(VP9_COMP *cpi, VP9_COMMON *cm, MACROBLOCK *x) {
diff --git a/vp9/encoder/vp9_segmentation.h b/vp9/encoder/vp9_segmentation.h
index 3d963f1d5..589c04bbd 100644
--- a/vp9/encoder/vp9_segmentation.h
+++ b/vp9/encoder/vp9_segmentation.h
@@ -11,7 +11,7 @@
 
 #include "string.h"
 #include "vp9/common/vp9_blockd.h"
-#include "vp9_onyx_int.h"
+#include "vp9/encoder/vp9_onyx_int.h"
 
 #ifndef __INC_SEGMENTATION_H__
 #define __INC_SEGMENTATION_H__ 1
diff --git a/vp9/encoder/vp9_ssim.c b/vp9/encoder/vp9_ssim.c
index 71ea02e08..4cbb9149b 100644
--- a/vp9/encoder/vp9_ssim.c
+++ b/vp9/encoder/vp9_ssim.c
@@ -9,7 +9,7 @@
  */
 
 
-#include "vp9_onyx_int.h"
+#include "vp9/encoder/vp9_onyx_int.h"
 
 void vp9_ssim_parms_16x16_c(unsigned char *s, int sp, unsigned char *r,
                             int rp, unsigned long *sum_s, unsigned long *sum_r,
diff --git a/vp9/encoder/vp9_temporal_filter.c b/vp9/encoder/vp9_temporal_filter.c
index c8fc6b7d0..44f0a623e 100644
--- a/vp9/encoder/vp9_temporal_filter.c
+++ b/vp9/encoder/vp9_temporal_filter.c
@@ -10,18 +10,18 @@
 
 
 #include "vp9/common/vp9_onyxc_int.h"
-#include "vp9_onyx_int.h"
+#include "vp9/encoder/vp9_onyx_int.h"
 #include "vp9/common/vp9_systemdependent.h"
-#include "vp9_quantize.h"
+#include "vp9/encoder/vp9_quantize.h"
 #include "vp9/common/vp9_alloccommon.h"
-#include "vp9_mcomp.h"
-#include "vp9_firstpass.h"
-#include "vp9_psnr.h"
+#include "vp9/encoder/vp9_mcomp.h"
+#include "vp9/encoder/vp9_firstpass.h"
+#include "vp9/encoder/vp9_psnr.h"
 #include "vpx_scale/vpxscale.h"
 #include "vp9/common/vp9_extend.h"
-#include "vp9_ratectrl.h"
+#include "vp9/encoder/vp9_ratectrl.h"
 #include "vp9/common/vp9_quant_common.h"
-#include "vp9_segmentation.h"
+#include "vp9/encoder/vp9_segmentation.h"
 #include "vpx_mem/vpx_mem.h"
 #include "vp9/common/vp9_swapyv12buffer.h"
 #include "vpx_ports/vpx_timer.h"
diff --git a/vp9/encoder/vp9_tokenize.c b/vp9/encoder/vp9_tokenize.c
index 1713cdb73..41b7f0edf 100644
--- a/vp9/encoder/vp9_tokenize.c
+++ b/vp9/encoder/vp9_tokenize.c
@@ -13,8 +13,8 @@
 #include <stdio.h>
 #include <string.h>
 #include <assert.h>
-#include "vp9_onyx_int.h"
-#include "vp9_tokenize.h"
+#include "vp9/encoder/vp9_onyx_int.h"
+#include "vp9/encoder/vp9_tokenize.h"
 #include "vpx_mem/vpx_mem.h"
 
 #include "vp9/common/vp9_pred_common.h"
diff --git a/vp9/encoder/vp9_tokenize.h b/vp9/encoder/vp9_tokenize.h
index e69d8f633..9ac26eb1c 100644
--- a/vp9/encoder/vp9_tokenize.h
+++ b/vp9/encoder/vp9_tokenize.h
@@ -13,7 +13,7 @@
 #define tokenize_h
 
 #include "vp9/common/vp9_entropy.h"
-#include "vp9_block.h"
+#include "vp9/encoder/vp9_block.h"
 
 void vp9_tokenize_initialize();
 
diff --git a/vp9/encoder/vp9_treewriter.c b/vp9/encoder/vp9_treewriter.c
index 4bdf473db..8e252813c 100644
--- a/vp9/encoder/vp9_treewriter.c
+++ b/vp9/encoder/vp9_treewriter.c
@@ -9,7 +9,7 @@
  */
 
 
-#include "vp9_treewriter.h"
+#include "vp9/encoder/vp9_treewriter.h"
 
 static void cost(
   int *const C,
diff --git a/vp9/encoder/vp9_treewriter.h b/vp9/encoder/vp9_treewriter.h
index d9198afcf..2175c744b 100644
--- a/vp9/encoder/vp9_treewriter.h
+++ b/vp9/encoder/vp9_treewriter.h
@@ -17,7 +17,7 @@
 
 #include "vp9/common/vp9_treecoder.h"
 
-#include "vp9_boolhuff.h"       /* for now */
+#include "vp9/encoder/vp9_boolhuff.h"       /* for now */
 
 typedef BOOL_CODER vp9_writer;
 
diff --git a/vp9/encoder/vp9_variance_c.c b/vp9/encoder/vp9_variance_c.c
index 278c7ebbe..a91cb122c 100644
--- a/vp9/encoder/vp9_variance_c.c
+++ b/vp9/encoder/vp9_variance_c.c
@@ -9,7 +9,7 @@
  */
 
 
-#include "vp9_variance.h"
+#include "vp9/encoder/vp9_variance.h"
 #include "vp9/common/vp9_filter.h"
 #include "vp9/common/vp9_subpelvar.h"
 #include "vpx/vpx_integer.h"