diff --git a/src/libostree/ostree-sysroot-deploy.c b/src/libostree/ostree-sysroot-deploy.c
index 32078505..7e72a3ef 100644
--- a/src/libostree/ostree-sysroot-deploy.c
+++ b/src/libostree/ostree-sysroot-deploy.c
@@ -113,7 +113,7 @@ hardlink_or_copy_at (int         src_dfd,
                                   sysroot_flags_to_copy_flags (0, flags),
                                   cancellable, error);
       else
-        return glnx_throw_errno_prefix (error, "linkat");
+        return glnx_throw_errno_prefix (error, "linkat(%s)", dest_subpath);
     }
 
   return TRUE;
@@ -868,16 +868,29 @@ ostree_sysroot_write_origin_file (OstreeSysroot         *sysroot,
                                      cancellable, error);
 }
 
+/* Originally OSTree defined kernels to be found underneath /boot
+ * in the tree.  But that means when mounting /boot at runtime
+ * we end up masking the content underneath, triggering a warning.
+ *
+ * For that reason, and also consistency with the "/usr defines the OS" model we
+ * later switched to defining the in-tree kernels to be found under
+ * /usr/lib/ostree-boot.
+ */
 static gboolean
 get_kernel_from_tree (int             deployment_dfd,
                       int            *out_boot_dfd,
-                      char          **out_kernel_name,
-                      char          **out_initramfs_name,
+                      char          **out_kernel_srcpath,
+                      char          **out_kernel_namever,
+                      char          **out_initramfs_srcpath,
+                      char          **out_initramfs_namever,
+                      char          **out_bootcsum,
                       GCancellable   *cancellable,
                       GError        **error)
 {
-  g_autofree char *ret_kernel_name = NULL;
-  g_autofree char *ret_initramfs_name = NULL;
+  g_autofree char *ret_kernel_srcpath = NULL;
+  g_autofree char *ret_kernel_namever = NULL;
+  g_autofree char *ret_initramfs_srcpath = NULL;
+  g_autofree char *ret_initramfs_namever = NULL;
   g_autofree char *kernel_checksum = NULL;
   g_autofree char *initramfs_checksum = NULL;
 
@@ -907,67 +920,57 @@ get_kernel_from_tree (int             deployment_dfd,
       if (dent == NULL)
         break;
 
-      if (ret_kernel_name == NULL && g_str_has_prefix (dent->d_name, "vmlinuz-"))
+      const char *name = dent->d_name;
+      if (ret_kernel_srcpath == NULL && g_str_has_prefix (name, "vmlinuz-"))
         {
-          const char *dash = strrchr (dent->d_name, '-');
+          const char *dash = strrchr (name, '-');
           g_assert (dash);
           if (ostree_validate_structureof_checksum_string (dash + 1, NULL))
             {
               kernel_checksum = g_strdup (dash + 1);
-              ret_kernel_name = g_strdup (dent->d_name);
+              ret_kernel_srcpath = g_strdup (name);
+              ret_kernel_namever = g_strndup (name, dash - name);
             }
         }
-      else if (ret_initramfs_name == NULL && g_str_has_prefix (dent->d_name, "initramfs-"))
+      else if (ret_initramfs_srcpath == NULL && g_str_has_prefix (name, "initramfs-"))
         {
-          const char *dash = strrchr (dent->d_name, '-');
+          const char *dash = strrchr (name, '-');
           g_assert (dash);
           if (ostree_validate_structureof_checksum_string (dash + 1, NULL))
             {
               initramfs_checksum = g_strdup (dash + 1);
-              ret_initramfs_name = g_strdup (dent->d_name);
+              ret_initramfs_srcpath = g_strdup (name);
+              ret_initramfs_namever = g_strndup (name, dash - name);
             }
         }
 
-      if (ret_kernel_name != NULL && ret_initramfs_name != NULL)
+      if (ret_kernel_srcpath != NULL && ret_initramfs_srcpath != NULL)
         break;
     }
 
-  if (ret_kernel_name == NULL)
+  if (ret_kernel_srcpath == NULL)
     {
       g_set_error (error, G_IO_ERROR, G_IO_ERROR_NOT_FOUND,
-                   "Failed to find boot/vmlinuz-<CHECKSUM> in tree");
+                   "Failed to find kernel in /usr/lib/ostree-boot or /boot");
       return FALSE;
     }
 
-  if (ret_initramfs_name != NULL)
+  if (ret_initramfs_srcpath != NULL)
     {
       if (strcmp (kernel_checksum, initramfs_checksum) != 0)
         {
           g_set_error (error, G_IO_ERROR, G_IO_ERROR_NOT_FOUND,
-                       "Mismatched kernel checksum vs initrd in tree");
+                       "Mismatched kernel checksum vs initrd");
           return FALSE;
         }
     }
 
   *out_boot_dfd = glnx_steal_fd (&ret_boot_dfd);
-  *out_kernel_name = g_steal_pointer (&ret_kernel_name);
-  *out_initramfs_name = g_steal_pointer (&ret_initramfs_name);
-  return TRUE;
-}
-
-static gboolean
-checksum_from_kernel_src (const char   *name,
-                          char        **out_checksum,
-                          GError     **error)
-{
-  const char *last_dash = strrchr (name, '-');
-  if (!last_dash)
-    {
-      return glnx_throw (error,
-                        "Malformed kernel/initramfs name '%s', missing '-'",
-                        name);
-    }
-  *out_checksum = g_strdup (last_dash + 1);
+  *out_kernel_srcpath = g_steal_pointer (&ret_kernel_srcpath);
+  *out_kernel_namever = g_steal_pointer (&ret_kernel_namever);
+  *out_initramfs_srcpath = g_steal_pointer (&ret_initramfs_srcpath);
+  *out_initramfs_namever = g_steal_pointer (&ret_initramfs_namever);
+  *out_bootcsum = g_steal_pointer (&kernel_checksum);
   return TRUE;
 }
 
@@ -1231,15 +1234,6 @@ swap_bootlinks (OstreeSysroot *self,
   return TRUE;
 }
 
-static char *
-remove_checksum_from_kernel_name (const char *name,
-                                  const char *csum)
-{
-  const char *p = strrchr (name, '-');
-  g_assert_cmpstr (p+1, ==, csum);
-  return g_strndup (name, p-name);
-}
-
 static GHashTable *
 parse_os_release (const char *contents,
                   const char *split)
@@ -1293,11 +1287,19 @@ install_deployment_kernel (OstreeSysroot   *sysroot,
                        &deployment_dfd, error))
     return FALSE;
 
+  /* Find the kernel/initramfs in the tree */
   glnx_fd_close int tree_boot_dfd = -1;
-  g_autofree char *tree_kernel_name = NULL;
-  g_autofree char *tree_initramfs_name = NULL;
+  g_autofree char *tree_kernel_srcpath = NULL;
+  g_autofree char *tree_kernel_namever = NULL;
+  g_autofree char *tree_initramfs_srcpath = NULL;
+  g_autofree char *tree_initramfs_namever = NULL;
+  g_autofree char *tree_bootcsum = NULL;
   if (!get_kernel_from_tree (deployment_dfd, &tree_boot_dfd,
-                             &tree_kernel_name, &tree_initramfs_name,
+                             &tree_kernel_srcpath,
+                             &tree_kernel_namever,
+                             &tree_initramfs_srcpath,
+                             &tree_initramfs_namever,
+                             &tree_bootcsum,
                              cancellable, error))
     return FALSE;
 
@@ -1307,6 +1309,7 @@ install_deployment_kernel (OstreeSysroot   *sysroot,
 
   const char *osname = ostree_deployment_get_osname (deployment);
   const char *bootcsum = ostree_deployment_get_bootcsum (deployment);
+  g_assert_cmpstr (bootcsum, ==, tree_bootcsum);
   g_autofree char *bootcsumdir = g_strdup_printf ("ostree/%s-%s", osname, bootcsum);
   g_autofree char *bootconfdir = g_strdup_printf ("loader.%d/entries", new_bootversion);
   g_autofree char *bootconf_name = g_strdup_printf ("ostree-%s-%d.conf", osname,
@@ -1321,30 +1324,33 @@ install_deployment_kernel (OstreeSysroot   *sysroot,
   if (!glnx_shutil_mkdir_p_at (boot_dfd, bootconfdir, 0775, cancellable, error))
     return FALSE;
 
-  g_autofree char *dest_kernel_name = remove_checksum_from_kernel_name (tree_kernel_name, bootcsum);
+  /* Install (hardlink/copy) the kernel into /boot/ostree/osname-${bootcsum} if
+   * it doesn't exist already.
+   */
   struct stat stbuf;
-  if (fstatat (bootcsum_dfd, dest_kernel_name, &stbuf, 0) != 0)
+  if (fstatat (bootcsum_dfd, tree_kernel_namever, &stbuf, 0) != 0)
     {
       if (errno != ENOENT)
-        return glnx_throw_errno_prefix (error, "fstat %s", dest_kernel_name);
-      if (!hardlink_or_copy_at (tree_boot_dfd, tree_kernel_name,
-                                bootcsum_dfd, dest_kernel_name,
+        return glnx_throw_errno_prefix (error, "fstat %s", tree_kernel_namever);
+      if (!hardlink_or_copy_at (tree_boot_dfd, tree_kernel_srcpath,
+                                bootcsum_dfd, tree_kernel_namever,
                                 sysroot->debug_flags,
                                 cancellable, error))
         return FALSE;
     }
 
-  g_autofree char *dest_initramfs_name = NULL;
-  if (tree_initramfs_name)
+  /* If we have an initramfs, then install it into
+   * /boot/ostree/osname-${bootcsum} if it doesn't exist already.
+   */
+  if (tree_initramfs_srcpath)
     {
-      dest_initramfs_name = remove_checksum_from_kernel_name (tree_initramfs_name, bootcsum);
-
-      if (fstatat (bootcsum_dfd, dest_initramfs_name, &stbuf, 0) != 0)
+      g_assert (tree_initramfs_namever);
+      if (fstatat (bootcsum_dfd, tree_initramfs_namever, &stbuf, 0) != 0)
         {
           if (errno != ENOENT)
-            return glnx_throw_errno_prefix (error, "fstat %s", dest_initramfs_name);
-          if (!hardlink_or_copy_at (tree_boot_dfd, tree_initramfs_name,
-                                    bootcsum_dfd, dest_initramfs_name,
+            return glnx_throw_errno_prefix (error, "fstat %s", tree_initramfs_namever);
+          if (!hardlink_or_copy_at (tree_boot_dfd, tree_initramfs_srcpath,
+                                    bootcsum_dfd, tree_initramfs_namever,
                                     sysroot->debug_flags,
                                     cancellable, error))
             return FALSE;
@@ -1425,12 +1431,12 @@ install_deployment_kernel (OstreeSysroot   *sysroot,
 
   g_autofree char *version_key = g_strdup_printf ("%d", n_deployments - ostree_deployment_get_index (deployment));
   ostree_bootconfig_parser_set (bootconfig, OSTREE_COMMIT_META_KEY_VERSION, version_key);
-  g_autofree char * boot_relpath = g_strconcat ("/", bootcsumdir, "/", dest_kernel_name, NULL);
+  g_autofree char * boot_relpath = g_strconcat ("/", bootcsumdir, "/", tree_kernel_namever, NULL);
   ostree_bootconfig_parser_set (bootconfig, "linux", boot_relpath);
 
-  if (dest_initramfs_name)
+  if (tree_initramfs_namever)
     {
-      g_autofree char * boot_relpath = g_strconcat ("/", bootcsumdir, "/", dest_initramfs_name, NULL);
+      g_autofree char * boot_relpath = g_strconcat ("/", bootcsumdir, "/", tree_initramfs_namever, NULL);
       ostree_bootconfig_parser_set (bootconfig, "initrd", boot_relpath);
     }
 
@@ -2053,24 +2059,20 @@ ostree_sysroot_deploy_tree (OstreeSysroot     *self,
     }
 
   glnx_fd_close int tree_boot_dfd = -1;
-  g_autofree char *tree_kernel_path = NULL;
-  g_autofree char *tree_initramfs_path = NULL;
+  g_autofree char *tree_kernel_srcpath = NULL;
+  g_autofree char *tree_kernel_namever = NULL;
+  g_autofree char *tree_initramfs_srcpath = NULL;
+  g_autofree char *tree_initramfs_namever = NULL;
+  g_autofree char *tree_bootcsum = NULL;
   if (!get_kernel_from_tree (deployment_dfd, &tree_boot_dfd,
-                             &tree_kernel_path, &tree_initramfs_path,
+                             &tree_kernel_srcpath,
+                             &tree_kernel_namever,
+                             &tree_initramfs_srcpath,
+                             &tree_initramfs_namever,
+                             &new_bootcsum,
                              cancellable, error))
     return FALSE;
 
-  if (tree_initramfs_path != NULL)
-    {
-      if (!checksum_from_kernel_src (tree_initramfs_path, &new_bootcsum, error))
-        return FALSE;
-    }
-  else
-    {
-      if (!checksum_from_kernel_src (tree_kernel_path, &new_bootcsum, error))
-        return FALSE;
-    }
-
   _ostree_deployment_set_bootcsum (new_deployment, new_bootcsum);
 
   /* Create an empty boot configuration; we will merge things into
diff --git a/tests/libtest.sh b/tests/libtest.sh
index 6f33c5b5..ff096505 100755
--- a/tests/libtest.sh
+++ b/tests/libtest.sh
@@ -363,8 +363,10 @@ setup_os_boot_grub2() {
 
 setup_os_repository () {
     mode=$1
-    bootmode=$2
     shift
+    bootmode=$1
+    shift
+    bootdir=${1:-usr/lib/ostree-boot}
 
     oldpwd=`pwd`
 
@@ -379,14 +381,19 @@ setup_os_repository () {
     cd ${test_tmpdir}
     mkdir osdata
     cd osdata
-    mkdir -p boot usr/bin usr/lib/modules/3.6.0 usr/share usr/etc
-    echo "a kernel" > boot/vmlinuz-3.6.0
-    echo "an initramfs" > boot/initramfs-3.6.0
-    bootcsum=$(cat boot/vmlinuz-3.6.0 boot/initramfs-3.6.0 | sha256sum | cut -f 1 -d ' ')
+    mkdir -p usr/bin usr/lib/modules/3.6.0 usr/share usr/etc
+    mkdir -p ${bootdir}
+    echo "a kernel" > ${bootdir}/vmlinuz-3.6.0
+    echo "an initramfs" > ${bootdir}/initramfs-3.6.0
+    bootcsum=$(cat ${bootdir}/vmlinuz-3.6.0 ${bootdir}/initramfs-3.6.0 | sha256sum | cut -f 1 -d ' ')
     export bootcsum
-    mv boot/vmlinuz-3.6.0 boot/vmlinuz-3.6.0-${bootcsum}
-    mv boot/initramfs-3.6.0 boot/initramfs-3.6.0-${bootcsum}
-    
+    # Add the checksum for legacy dirs (/boot, /usr/lib/ostree-boot), but not
+    # /usr/lib/modules.
+    if [[ $bootdir != usr/lib/modules ]]; then
+        mv ${bootdir}/vmlinuz-3.6.0{,-${bootcsum}}
+        mv ${bootdir}/initramfs-3.6.0{,-${bootcsum}}
+    fi
+
     echo "an executable" > usr/bin/sh
     echo "some shared data" > usr/share/langs.txt
     echo "a library" > usr/lib/libfoo.so.0
@@ -458,13 +465,17 @@ os_repository_new_commit ()
     branch=${3:-testos/buildmaster/x86_64-runtime}
     echo "BOOT ITERATION: $boot_checksum_iteration"
     cd ${test_tmpdir}/osdata
-    rm boot/*
-    echo "new: a kernel ${boot_checksum_iteration}" > boot/vmlinuz-3.6.0
-    echo "new: an initramfs ${boot_checksum_iteration}" > boot/initramfs-3.6.0
-    bootcsum=$(cat boot/vmlinuz-3.6.0 boot/initramfs-3.6.0 | sha256sum | cut -f 1 -d ' ')
+    bootdir=usr/lib/ostree-boot
+    if ! test -d ${bootdir}; then
+        bootdir=boot
+    fi
+    rm ${bootdir}/*
+    echo "new: a kernel ${boot_checksum_iteration}" > ${bootdir}/vmlinuz-3.6.0
+    echo "new: an initramfs ${boot_checksum_iteration}" > ${bootdir}/initramfs-3.6.0
+    bootcsum=$(cat ${bootdir}/vmlinuz-3.6.0 ${bootdir}/initramfs-3.6.0 | sha256sum | cut -f 1 -d ' ')
     export bootcsum
-    mv boot/vmlinuz-3.6.0 boot/vmlinuz-3.6.0-${bootcsum}
-    mv boot/initramfs-3.6.0 boot/initramfs-3.6.0-${bootcsum}
+    mv ${bootdir}/vmlinuz-3.6.0 ${bootdir}/vmlinuz-3.6.0-${bootcsum}
+    mv ${bootdir}/initramfs-3.6.0 ${bootdir}/initramfs-3.6.0-${bootcsum}
 
     echo "a new default config file" > usr/etc/a-new-default-config-file
     mkdir -p usr/etc/new-default-dir
diff --git a/tests/test-admin-deploy-syslinux.sh b/tests/test-admin-deploy-syslinux.sh
index e03e211b..b19a74f0 100755
--- a/tests/test-admin-deploy-syslinux.sh
+++ b/tests/test-admin-deploy-syslinux.sh
@@ -19,7 +19,7 @@
 
 set -euo pipefail
 
-echo "1..19"
+echo "1..20"
 
 . $(dirname $0)/libtest.sh
 
@@ -27,3 +27,23 @@ echo "1..19"
 setup_os_repository "archive-z2" "syslinux"
 
 . $(dirname $0)/admin-test.sh
+
+cd ${test_tmpdir}
+rm httpd osdata testos-repo sysroot -rf
+setup_os_repository "archive-z2" "syslinux" "boot"
+
+${CMD_PREFIX} ostree --repo=sysroot/ostree/repo pull-local --remote=testos testos-repo testos/buildmaster/x86_64-runtime
+rev=$(${CMD_PREFIX} ostree --repo=sysroot/ostree/repo rev-parse testos/buildmaster/x86_64-runtime)
+${CMD_PREFIX} ostree admin deploy --karg=root=LABEL=MOO --karg=quiet --os=testos testos:testos/buildmaster/x86_64-runtime
+assert_file_has_content sysroot/boot/loader/entries/ostree-testos-0.conf 'options.* root=LABEL=MOO'
+assert_file_has_content sysroot/boot/loader/entries/ostree-testos-0.conf 'options.* quiet'
+assert_file_has_content sysroot/boot/ostree/testos-${bootcsum}/vmlinuz-3.6.0 'a kernel'
+assert_file_has_content sysroot/boot/ostree/testos-${bootcsum}/initramfs-3.6.0 'an initramfs'
+# kernel/initrams should also be in the tree's /boot with the checksum
+assert_file_has_content sysroot/ostree/deploy/testos/deploy/${rev}.0/boot/vmlinuz-3.6.0-${bootcsum} 'a kernel'
+assert_file_has_content sysroot/ostree/deploy/testos/deploy/${rev}.0/boot/initramfs-3.6.0-${bootcsum} 'an initramfs'
+assert_file_has_content sysroot/ostree/deploy/testos/deploy/${rev}.0/etc/os-release 'NAME=TestOS'
+assert_file_has_content sysroot/ostree/boot.1/testos/${bootcsum}/0/etc/os-release 'NAME=TestOS'
+${CMD_PREFIX} ostree admin status
+validate_bootloader
+echo "ok kernel in tree's /boot"
diff --git a/tests/test-admin-deploy-uboot.sh b/tests/test-admin-deploy-uboot.sh
index 5262b48a..3685e31e 100755
--- a/tests/test-admin-deploy-uboot.sh
+++ b/tests/test-admin-deploy-uboot.sh
@@ -30,8 +30,7 @@ setup_os_repository "archive-z2" "uboot"
 . $(dirname $0)/admin-test.sh
 
 cd ${test_tmpdir}
-ln -s ../../boot/ osdata/usr/lib/ostree-boot
-cat << 'EOF' > osdata/boot/uEnv.txt
+cat << 'EOF' > osdata/usr/lib/ostree-boot/uEnv.txt
 loaduimage=load mmc ${bootpart} ${loadaddr} ${kernel_image}
 loadfdt=load mmc ${bootpart} ${fdtaddr} ${bootdir}${fdtfile}
 loadramdisk=load mmc ${bootpart} ${rdaddr} ${ramdisk_image}