After cloning Mesa git yesterday to a clean directory, this doesn't produce any errors:
$ ./autogen.sh --prefix=/usr/local/ --enable-texture-float --enable-dri3 --with-dri-driverdir=/usr/local/lib/dri --enable-shared-glapi --disable-llvm-shared-libs --disable-llvm --without-gallium-drivers --with-vulkan-drivers=intel --with-platforms=x11,drm,wayland --enable-gles2 --enable-gbm --disable-debug --with-dri-drivers="i965 swrast"

But with this:
$ make

I get:
----------------------------------------------------
  CC       wsi/wsi_common_display.lo
../../../src/vulkan/wsi/wsi_common_display.c:991:4: error: unknown field ‘sequence_handler’ specified in initializer
    .sequence_handler = wsi_display_sequence_handler,
    ^
../../../src/vulkan/wsi/wsi_common_display.c:991:24: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
    .sequence_handler = wsi_display_sequence_handler,
                        ^
../../../src/vulkan/wsi/wsi_common_display.c:991:24: note: (near initialization for ‘event_context.page_flip_handler’)
../../../src/vulkan/wsi/wsi_common_display.c: In function ‘wsi_register_vblank_event’:
../../../src/vulkan/wsi/wsi_common_display.c:1373:17: error: implicit declaration of function ‘drmCrtcQueueSequence’ [-Werror=implicit-function-declaration]
       int ret = drmCrtcQueueSequence(wsi->fd, connector->crtc_id,
                 ^
../../../src/vulkan/wsi/wsi_common_display.c: In function ‘wsi_acquire_xlib_display’:
../../../src/vulkan/wsi/wsi_common_display.c:2164:4: error: unknown type name ‘xcb_randr_lease_t’
    xcb_randr_lease_t lease = xcb_generate_id(connection);
    ^
../../../src/vulkan/wsi/wsi_common_display.c:2165:4: error: unknown type name ‘xcb_randr_create_lease_cookie_t’
    xcb_randr_create_lease_cookie_t cl_c =
    ^
../../../src/vulkan/wsi/wsi_common_display.c:2166:7: error: implicit declaration of function ‘xcb_randr_create_lease’ [-Werror=implicit-function-declaration]
       xcb_randr_create_lease(connection, root, lease, 1, 1,
       ^
../../../src/vulkan/wsi/wsi_common_display.c:2168:4: error: unknown type name ‘xcb_randr_create_lease_reply_t’
    xcb_randr_create_lease_reply_t *cl_r =
    ^
../../../src/vulkan/wsi/wsi_common_display.c:2169:7: error: implicit declaration of function ‘xcb_randr_create_lease_reply’ [-Werror=implicit-function-declaration]
       xcb_randr_create_lease_reply(connection, cl_c, NULL);
       ^
../../../src/vulkan/wsi/wsi_common_display.c:2169:7: warning: initialization makes pointer from integer without a cast [-Wint-conversion]
../../../src/vulkan/wsi/wsi_common_display.c:2174:12: error: request for member ‘nfd’ in something not a structure or union
    if (cl_r->nfd > 0) {
            ^
../../../src/vulkan/wsi/wsi_common_display.c:2175:20: error: implicit declaration of function ‘xcb_randr_create_lease_reply_fds’ [-Werror=implicit-function-declaration]
       int *rcl_f = xcb_randr_create_lease_reply_fds(connection, cl_r);
                    ^
../../../src/vulkan/wsi/wsi_common_display.c:2175:20: warning: initialization makes pointer from integer without a cast [-Wint-conversion]
../../../src/vulkan/wsi/wsi_common_display.c: In function ‘wsi_get_swapchain_counter’:
../../../src/vulkan/wsi/wsi_common_display.c:2313:14: error: implicit declaration of function ‘drmCrtcGetSequence’ [-Werror=implicit-function-declaration]
    int ret = drmCrtcGetSequence(wsi->fd, connector->crtc_id, value, NULL);
              ^
cc1: some warnings being treated as errors
----------------------------------------------------

"drmCrtcGetSequence" can be found from xf86drm.h header in latest libdrm, not from the one in Ubuntu 16.04.

xcb_randr_* can be found from randr.h header in latest libxcb, not from the one in Ubuntu 16.04 (bew libxcb needs just newer xcb-proto).

-> dependency checks need to be updated.