Index: lib/Tooling/JSONCompilationDatabase.cpp
===================================================================
--- lib/Tooling/JSONCompilationDatabase.cpp
+++ lib/Tooling/JSONCompilationDatabase.cpp
@@ -20,6 +20,7 @@
 #include "llvm/Support/CommandLine.h"
 #include "llvm/Support/Path.h"
 #include "llvm/Support/StringSaver.h"
+#include <set>
 #include <system_error>
 
 namespace clang {
@@ -251,20 +252,64 @@
   return Arguments;
 }
 
+static std::vector<std::string>
+deduplicateCommandLine(const std::vector<std::string> &Nodes) {
+  struct FlagFilter {
+    private:
+      int State;
+      const std::map<std::string, int> Flags = {
+        {"-MD", 0}, {"-MMD", 0}, {"-MG", 0}, {"-MP", 0}, {"-MF", 1}, {"-MT", 1}, {"-MQ", 1}
+      };
+    public:
+      FlagFilter() : State(0) { }
+
+      bool operator()(const std::string &Current) {
+        if (State != 0) {
+          --State;
+          return false;
+        }
+        const auto Check = Flags.find(Current);
+        if (Check != Flags.end()) {
+          State = Check->second;
+          return false;
+        }
+        return true;
+      }
+  };
+
+  std::vector<std::string> Result;
+  std::copy_if(Nodes.begin(), Nodes.end(), std::back_inserter(Result), FlagFilter());
+  return Result;
+}
+
+struct CompareCompileCommand {
+  bool operator()(const CompileCommand &Lhs, const CompileCommand &Rhs) const {
+    return (Lhs.Directory == Rhs.Directory) &&
+           (Lhs.Filename == Rhs.Filename) &&
+           (Lhs.CommandLine == Rhs.CommandLine) &&
+           (Lhs.Output == Rhs.Output);
+  }
+};
+
 void JSONCompilationDatabase::getCommands(
     ArrayRef<CompileCommandRef> CommandsRef,
     std::vector<CompileCommand> &Commands) const {
+  // To filter out duplicate elements put the result first into a set.
+  std::set<CompileCommand, CompareCompileCommand> Results;
   for (int I = 0, E = CommandsRef.size(); I != E; ++I) {
     SmallString<8> DirectoryStorage;
     SmallString<32> FilenameStorage;
     SmallString<32> OutputStorage;
     auto Output = std::get<3>(CommandsRef[I]);
-    Commands.emplace_back(
+    Results.emplace(
         std::get<0>(CommandsRef[I])->getValue(DirectoryStorage),
         std::get<1>(CommandsRef[I])->getValue(FilenameStorage),
-        nodeToCommandLine(Syntax, std::get<2>(CommandsRef[I])),
+        deduplicateCommandLine(
+          nodeToCommandLine(Syntax, std::get<2>(CommandsRef[I]))),
         Output ? Output->getValue(OutputStorage) : "");
   }
+  // Copy the unique elements into the real return value.
+  std::copy(Results.begin(), Results.end(), std::back_inserter(Commands));
 }
 
 bool JSONCompilationDatabase::parse(std::string &ErrorMessage) {