diff --git a/cmd/soong_build/main.go b/cmd/soong_build/main.go
index beda184..16a4e1a 100644
--- a/cmd/soong_build/main.go
+++ b/cmd/soong_build/main.go
@@ -58,30 +58,32 @@
 	flag.StringVar(&outDir, "out", "", "Soong output directory (usually $TOP/out/soong)")
 	flag.StringVar(&availableEnvFile, "available_env", "", "File containing available environment variables")
 	flag.StringVar(&usedEnvFile, "used_env", "", "File containing used environment variables")
+	flag.StringVar(&globFile, "globFile", "build-globs.ninja", "the Ninja file of globs to output")
+	flag.StringVar(&globListDir, "globListDir", "", "the directory containing the glob list files")
+	flag.StringVar(&cmdlineArgs.SoongOutDir, "b", ".", "the build output directory")
+	flag.StringVar(&cmdlineArgs.OutDir, "n", "", "the ninja builddir directory")
+	flag.StringVar(&cmdlineArgs.ModuleListFile, "l", "", "file that lists filepaths to parse")
 
 	// Debug flags
 	flag.StringVar(&delveListen, "delve_listen", "", "Delve port to listen on for debugging")
 	flag.StringVar(&delvePath, "delve_path", "", "Path to Delve. Only used if --delve_listen is set")
+	flag.StringVar(&cmdlineArgs.Cpuprofile, "cpuprofile", "", "write cpu profile to file")
+	flag.StringVar(&cmdlineArgs.TraceFile, "trace", "", "write trace to file")
+	flag.StringVar(&cmdlineArgs.Memprofile, "memprofile", "", "write memory profile to file")
+	flag.BoolVar(&cmdlineArgs.NoGC, "nogc", false, "turn off GC for debugging")
 
 	// Flags representing various modes soong_build can run in
 	flag.StringVar(&moduleGraphFile, "module_graph_file", "", "JSON module graph file to output")
 	flag.StringVar(&docFile, "soong_docs", "", "build documentation file to output")
 	flag.StringVar(&bazelQueryViewDir, "bazel_queryview_dir", "", "path to the bazel queryview directory relative to --top")
 	flag.StringVar(&bp2buildMarker, "bp2build_marker", "", "If set, run bp2build, touch the specified marker file then exit")
-
 	flag.StringVar(&cmdlineArgs.OutFile, "o", "build.ninja", "the Ninja file to output")
-	flag.StringVar(&globFile, "globFile", "build-globs.ninja", "the Ninja file of globs to output")
-	flag.StringVar(&globListDir, "globListDir", "", "the directory containing the glob list files")
-	flag.StringVar(&cmdlineArgs.BuildDir, "b", ".", "the build output directory")
-	flag.StringVar(&cmdlineArgs.NinjaBuildDir, "n", "", "the ninja builddir directory")
-	flag.StringVar(&cmdlineArgs.Cpuprofile, "cpuprofile", "", "write cpu profile to file")
-	flag.StringVar(&cmdlineArgs.TraceFile, "trace", "", "write trace to file")
-	flag.StringVar(&cmdlineArgs.Memprofile, "memprofile", "", "write memory profile to file")
-	flag.BoolVar(&cmdlineArgs.NoGC, "nogc", false, "turn off GC for debugging")
+	flag.BoolVar(&cmdlineArgs.EmptyNinjaFile, "empty-ninja-file", false, "write out a 0-byte ninja file")
+
+	// Flags that probably shouldn't be flags of soong_build but we haven't found
+	// the time to remove them yet
 	flag.BoolVar(&cmdlineArgs.RunGoTests, "t", false, "build and run go tests during bootstrap")
 	flag.BoolVar(&cmdlineArgs.UseValidations, "use-validations", false, "use validations to depend on go tests")
-	flag.StringVar(&cmdlineArgs.ModuleListFile, "l", "", "file that lists filepaths to parse")
-	flag.BoolVar(&cmdlineArgs.EmptyNinjaFile, "empty-ninja-file", false, "write out a 0-byte ninja file")
 }
 
 func newNameResolver(config android.Config) *android.NameResolver {
@@ -503,8 +505,8 @@
 		"bazel-" + filepath.Base(topDir),
 	}
 
-	if cmdlineArgs.NinjaBuildDir[0] != '/' {
-		excludes = append(excludes, cmdlineArgs.NinjaBuildDir)
+	if cmdlineArgs.OutDir[0] != '/' {
+		excludes = append(excludes, cmdlineArgs.OutDir)
 	}
 
 	existingBazelRelatedFiles, err := getExistingBazelRelatedFiles(topDir)