diff --git a/src/project.cc b/src/project.cc
index 2bf8c4f7..00518ddf 100644
--- a/src/project.cc
+++ b/src/project.cc
@@ -52,10 +52,15 @@ static std::vector<std::string> kBlacklistMulti = {
 
 // Blacklisted flags which are always removed from the command line.
 static std::vector<std::string> kBlacklist = {
-    "-c", "-MP", "-MD", "-MMD", "--fcolor-diagnostics",
+    "-c",
+    "-MP",
+    "-MD",
+    "-MMD",
+    "--fcolor-diagnostics",
 
     // This strips path-like args but is a bit hacky.
-    "/", "..",
+    "/",
+    "..",
 };
 
 // Arguments which are followed by a potentially relative path. We need to make
@@ -207,7 +212,9 @@ std::vector<Project::Entry> LoadFromDirectoryListing(ProjectConfig* config) {
 
   std::vector<std::string> args;
   std::cerr << "Using arguments: ";
-  for (const std::string& line : ReadLines(config->project_dir + "/.cquery")) {
+  for (std::string line :
+       ReadLinesWithEnding(config->project_dir + "/.cquery")) {
+    Trim(line);
     if (line.empty() || StartsWith(line, "#"))
       continue;
     if (!args.empty())
diff --git a/src/utils.cc b/src/utils.cc
index 0c8d2d2e..c568d8a0 100644
--- a/src/utils.cc
+++ b/src/utils.cc
@@ -245,7 +245,7 @@ optional<std::string> ReadContent(const std::string& filename) {
   }
 }
 
-std::vector<std::string> ReadLines(std::string filename) {
+std::vector<std::string> ReadLinesWithEnding(std::string filename) {
   std::vector<std::string> result;
 
   std::ifstream input(filename);
@@ -296,7 +296,7 @@ std::unordered_map<std::string, std::string> ParseTestExpectation(
   std::string active_output_filename;
   std::string active_output_contents;
 
-  for (std::string line_with_ending : ReadLines(filename)) {
+  for (std::string line_with_ending : ReadLinesWithEnding(filename)) {
     if (StartsWith(line_with_ending, "*/"))
       break;
 
diff --git a/src/utils.h b/src/utils.h
index a15575d9..0a4a8198 100644
--- a/src/utils.h
+++ b/src/utils.h
@@ -74,7 +74,7 @@ void EnsureEndsInSlash(std::string& path);
 std::string EscapeFileName(std::string path);
 
 optional<std::string> ReadContent(const std::string& filename);
-std::vector<std::string> ReadLines(std::string filename);
+std::vector<std::string> ReadLinesWithEnding(std::string filename);
 std::vector<std::string> ToLines(const std::string& content,
                                  bool trim_whitespace);