diff --git a/generator/BUILD.gn b/generator/BUILD.gn
new file mode 100644
index 0000000000..2970e2277c
--- /dev/null
+++ b/generator/BUILD.gn
@@ -0,0 +1,59 @@
+# Copyright 2019 The Dawn Authors
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import("../scripts/dawn_overrides_with_defaults.gni")
+import("dawn_generator.gni")
+
+# The list of directories in which to check for stale autogenerated files.
+# It should include the list of all directories in which we ever generated
+# files but we can't just put dawn_gen_root because there are more than
+# autogenerated sources there.
+_stale_dirs = [
+    "dawn",
+    "dawn_native",
+    "dawn_wire",
+    "mock",
+    "src"
+]
+
+_allowed_output_dirs_file = "${dawn_gen_root}/removed_stale_autogen_files.allowed_output_dirs"
+write_file(_allowed_output_dirs_file, dawn_allowed_gen_output_dirs)
+
+_stale_dirs_file = "${dawn_gen_root}/removed_stale_autogen_files.stale_dirs"
+write_file(_stale_dirs_file, _stale_dirs)
+
+_stamp_file = "${dawn_gen_root}/removed_stale_autogen_files.stamp"
+
+# An action that removes autogenerated files that aren't in allowed directories
+# see dawn_generator.gni for more details.
+action("remove_stale_autogen_files") {
+  script = "remove_files.py"
+  args = [
+    "--root-dir",
+    rebase_path(dawn_gen_root, root_build_dir),
+    "--allowed-output-dirs-file",
+    rebase_path(_allowed_output_dirs_file, root_build_dir),
+    "--stale-dirs-file",
+    rebase_path(_stale_dirs_file, root_build_dir),
+    "--stamp",
+    rebase_path(_stamp_file, root_build_dir),
+  ]
+
+  # Have the "list of file" inputs as a dependency so that the action reruns
+  # as soon as they change.
+  inputs = [_allowed_output_dirs_file, _stale_dirs_file]
+
+  # Output a stamp file so we don't re-run this action on every build.
+  outputs = [_stamp_file]
+}
diff --git a/generator/dawn_generator.gni b/generator/dawn_generator.gni
index fc728832c9..370fc2c70b 100644
--- a/generator/dawn_generator.gni
+++ b/generator/dawn_generator.gni
@@ -15,6 +15,28 @@
 import("../scripts/dawn_overrides_with_defaults.gni")
 import("generator_lib.gni")
 
+# Dawn used to put autogenerated files in a lot of different places. When we
+# started to move them around, some compilation issues arised because some
+# stale include files stayed in the build directory and were picked up.
+# To counter this, now Dawn does the following:
+#
+#  1. The generated output file directory structure has to match the structure
+#    of the source tree, starting at dawn_gen_root (gen/ or
+#    gen/third_party/dawn depending on where we are).
+#  2. src/include and dawn_gen_root/src/include has to match the structure of
+#    the source tree too.
+#  3. Dawn files must use include relative to src/ or src/include such as
+#    "dawn/dawn.h" or "dawn_native/backend/BackendStuff.h".
+#
+# The allowed list below ensure 1). Include directory rules for Dawn ensure 3)
+# and 2) is something we need to enforce in code review.
+#
+# However GN's toolchains automatically add some include directories for us
+# which breaks 3) slightly. To avoid stale headers in for example
+# dawn_gen_root/src/dawn/dawn/ to be picked up (instead of
+# dawn_gen_root/src/dawn), we have a special action that removes files in
+# disallowed gen directories.
+
 dawn_allowed_gen_output_dirs = [
   "src/dawn/",
   "src/dawn_native/",
@@ -40,9 +62,6 @@ dawn_allowed_gen_output_dirs = [
 #       "MyAwesomeTarget.cpp",
 #       "MyAwesomeTarget.h",
 #     ]
-#
-#     # Optional, use a custom generated file directory.
-#     custom_gen_dir = "${target_gen_dir}/.."
 #   }
 #
 # Using the generated files is done like so:
@@ -55,9 +74,19 @@ dawn_allowed_gen_output_dirs = [
 template("dawn_generator") {
   generator_lib_action(target_name) {
     forward_variables_from(invoker, "*")
+
+    # Set arguments required to find the python libraries for the generator
     generator_lib_dir = "${dawn_root}/generator"
     jinja2_path = dawn_jinja2_dir
+
+    # Force Dawn's autogenerated file structure to mirror exactly the source
+    # tree but start at ${dawn_gen_root} instead of ${dawn_root}
     allowed_output_dirs = dawn_allowed_gen_output_dirs
+    custom_gen_dir = dawn_gen_root
+
+    # Make sure that we delete stale autogenerated file in directories that are
+    # no longer used by code generation to avoid include conflicts.
+    deps = [ "${dawn_root}/generator:remove_stale_autogen_files" ]
   }
 }
 
diff --git a/generator/generator_lib.gni b/generator/generator_lib.gni
index 10c560d926..36ac72f2f6 100644
--- a/generator/generator_lib.gni
+++ b/generator/generator_lib.gni
@@ -24,6 +24,8 @@
 #   outputs: List of expected outputs, generation will fail if there is a
 #     mistmatch.
 #
+#   deps: additional deps for the code generation targets.
+#
 #   generator_lib_dir: directory where generator_lib.py is located.
 #
 #   custom_gen_dir: Optional custom target gen dir. Defaults to $target_gen_dir
@@ -138,6 +140,9 @@ template("generator_lib_action") {
     ]
     depfile = _json_tarball_depfile
     args = _generator_args
+    if (defined(invoker.deps)) {
+      deps = invoker.deps
+    }
   }
 
   # Extract the JSON tarball into the gen_dir
diff --git a/generator/remove_files.py b/generator/remove_files.py
new file mode 100644
index 0000000000..b143abee11
--- /dev/null
+++ b/generator/remove_files.py
@@ -0,0 +1,70 @@
+# Copyright 2019 The Dawn Authors
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import argparse, glob, os, sys
+
+def check_in_subdirectory(path, directory):
+    return path.startswith(directory) and not '/' in path[len(directory):]
+
+def check_is_allowed(path, allowed_dirs):
+    return any(check_in_subdirectory(path, directory) for directory in allowed_dirs)
+
+def get_all_files_in_dir(find_directory):
+    result = []
+    for (directory, _, files) in os.walk(find_directory):
+        result += [os.path.join(directory, filename) for filename in files]
+    return result
+
+def run():
+    # Parse command line arguments
+    parser = argparse.ArgumentParser(
+        description = "Removes stale autogenerated files from gen/ directories."
+    )
+    parser.add_argument('--root-dir', type=str, help='The root directory, all other paths in files are relative to it.')
+    parser.add_argument('--allowed-output-dirs-file', type=str, help='The file containing a list of allowed directories')
+    parser.add_argument('--stale-dirs-file', type=str, help='The file containing a list of directories to check for stale files')
+    parser.add_argument('--stamp', type=str, help='A stamp written once this script completes')
+    args = parser.parse_args()
+
+    root_dir = args.root_dir
+    stamp_file = args.stamp
+
+    # Load the list of allowed and stale directories
+    with open(args.allowed_output_dirs_file) as f:
+        allowed_dirs = set([os.path.join(root_dir, line.strip()) for line in f.readlines()])
+
+    for directory in allowed_dirs:
+        if not directory.endswith('/'):
+            print('Allowed directory entry "{}" doesn\'t end with /'.format(directory))
+            return 1
+
+    with open(args.stale_dirs_file) as f:
+        stale_dirs = set([line.strip() for line in f.readlines()])
+
+    # Remove all files in stale dirs that aren't in the allowed dirs.
+    for stale_dir in stale_dirs:
+        stale_dir = os.path.join(root_dir, stale_dir)
+
+        for candidate in get_all_files_in_dir(stale_dir):
+            if not check_is_allowed(candidate, allowed_dirs):
+                os.remove(candidate)
+
+    # Finished! Write the stamp file so ninja knows to not run this again.
+    with open(stamp_file, "w") as f:
+        f.write("")
+
+    return 0
+
+if __name__ == "__main__":
+    sys.exit(run())
diff --git a/scripts/dawn_overrides_with_defaults.gni b/scripts/dawn_overrides_with_defaults.gni
index 196a448b55..2a65be7b6e 100644
--- a/scripts/dawn_overrides_with_defaults.gni
+++ b/scripts/dawn_overrides_with_defaults.gni
@@ -27,6 +27,7 @@ if (!defined(dawn_standalone)) {
 if (!defined(dawn_root)) {
   dawn_root = get_path_info("..", "abspath")
 }
+dawn_gen_root = get_path_info("${dawn_root}", "gen_dir")
 
 if (!defined(dawn_jinja2_dir)) {
   dawn_jinja2_dir = "//third_party/jinja2"
diff --git a/src/dawn/BUILD.gn b/src/dawn/BUILD.gn
index 1d50b9da22..2b94ce540e 100644
--- a/src/dawn/BUILD.gn
+++ b/src/dawn/BUILD.gn
@@ -23,10 +23,6 @@ import("${dawn_root}/scripts/dawn_component.gni")
 
 dawn_json_generator("dawn_headers_gen") {
   target = "dawn_headers"
-
-  # Generate as if we were in the main BUILD.gn because that was historically
-  # the case and we can't move generated files without clobbering the build.
-  custom_gen_dir = "${target_gen_dir}/../.."
   outputs = [
     "src/include/dawn/dawncpp.h",
     "src/include/dawn/dawn.h",