diff --git a/aos/config.bzl b/aos/config.bzl
index d281027..faaf45a 100644
--- a/aos/config.bzl
+++ b/aos/config.bzl
@@ -41,22 +41,32 @@
 
     all_files = flatbuffers_depset.to_list() + src_depset.to_list()
     ctx.actions.run(
-        outputs = [config, stripped_config, binary_config],
+        outputs = [stripped_config, binary_config],
         inputs = all_files,
         arguments = ctx.attr.flags + [
-            config.path,
-            stripped_config.path,
-            binary_config.path,
+            "--stripped_output=" + stripped_config.path,
+            "--binary_output=" + binary_config.path,
             (ctx.label.workspace_root or ".") + "/" + ctx.files.src[0].short_path,
             ctx.bin_dir.path,
         ] + [f.path for f in flatbuffers_depset.to_list()],
         progress_message = "Flattening config",
         executable = ctx.executable._config_flattener,
     )
-    runfiles = ctx.runfiles(files = [config, stripped_config, binary_config])
+    ctx.actions.run(
+        outputs = [config],
+        inputs = all_files,
+        arguments = ctx.attr.flags + [
+            "--full_output=" + config.path,
+            (ctx.label.workspace_root or ".") + "/" + ctx.files.src[0].short_path,
+            ctx.bin_dir.path,
+        ] + [f.path for f in flatbuffers_depset.to_list()],
+        progress_message = "Flattening config",
+        executable = ctx.executable._config_flattener,
+    )
+    runfiles = ctx.runfiles(files = [stripped_config, binary_config])
     return [
         DefaultInfo(
-            files = depset([config, stripped_config, binary_config]),
+            files = depset([stripped_config, binary_config]),
             runfiles = runfiles,
         ),
         AosConfigInfo(
diff --git a/aos/config_flattener.cc b/aos/config_flattener.cc
index b089d24..8170a89 100644
--- a/aos/config_flattener.cc
+++ b/aos/config_flattener.cc
@@ -9,19 +9,25 @@
 #include "aos/json_to_flatbuffer.h"
 #include "aos/util/file.h"
 
+DEFINE_string(full_output, "",
+              "If provided, the path to write the full json configuration to.");
+DEFINE_string(
+    stripped_output, "",
+    "If provided, the path to write the stripped json configuration to.");
+DEFINE_string(
+    binary_output, "",
+    "If provided, the path to write the binary flatbuffer configuration to.");
+
 namespace aos {
 
 int Main(int argc, char **argv) {
-  CHECK_GE(argc, 6) << ": Too few arguments";
+  CHECK_GE(argc, 3) << ": Too few arguments";
 
-  const char *full_output = argv[1];
-  const char *stripped_output = argv[2];
-  const char *binary_output = argv[3];
-  const char *config_path = argv[4];
+  const char *config_path = argv[1];
   // In order to support not only importing things by absolute path, but also
   // importing the outputs of genrules (rather than just manually written
   // files), we need to tell ReadConfig where the generated files directory is.
-  const char *bazel_outs_directory = argv[5];
+  const char *bazel_outs_directory = argv[2];
 
   VLOG(1) << "Reading " << config_path;
   FlatbufferDetachedBuffer<Configuration> config =
@@ -38,7 +44,7 @@
 
   std::vector<aos::FlatbufferVector<reflection::Schema>> schemas;
 
-  for (int i = 6; i < argc; ++i) {
+  for (int i = 3; i < argc; ++i) {
     schemas.emplace_back(FileToFlatbuffer<reflection::Schema>(argv[i]));
   }
 
@@ -55,11 +61,17 @@
   // TODO(austin): Figure out how to squash the schemas onto 1 line so it is
   // easier to read?
   VLOG(1) << "Flattened config is " << merged_config_json;
-  util::WriteStringToFileOrDie(full_output, merged_config_json);
-  util::WriteStringToFileOrDie(
-      stripped_output,
-      FlatbufferToJson(&config.message(), {.multi_line = true}));
-  aos::WriteFlatbufferToFile(binary_output, merged_config);
+  if (!FLAGS_full_output.empty()) {
+    util::WriteStringToFileOrDie(FLAGS_full_output, merged_config_json);
+  }
+  if (!FLAGS_stripped_output.empty()) {
+    util::WriteStringToFileOrDie(
+        FLAGS_stripped_output,
+        FlatbufferToJson(&config.message(), {.multi_line = true}));
+  }
+  if (!FLAGS_binary_output.empty()) {
+    aos::WriteFlatbufferToFile(FLAGS_binary_output, merged_config);
+  }
   return 0;
 }