Index: cfe/trunk/lib/Sema/AnalysisBasedWarnings.cpp
===================================================================
--- cfe/trunk/lib/Sema/AnalysisBasedWarnings.cpp
+++ cfe/trunk/lib/Sema/AnalysisBasedWarnings.cpp
@@ -2080,10 +2080,10 @@
   //     time.
   DiagnosticsEngine &Diags = S.getDiagnostics();
 
-  // Do not do any analysis for declarations in system headers if we are
-  // going to just ignore them.
-  if (Diags.getSuppressSystemWarnings() &&
-      S.SourceMgr.isInSystemHeader(D->getLocation()))
+  // Do not do any analysis if we are going to just ignore them.
+  if (Diags.getIgnoreAllWarnings() ||
+      (Diags.getSuppressSystemWarnings() &&
+       S.SourceMgr.isInSystemHeader(D->getLocation())))
     return;
 
   // For code in dependent contexts, we'll do this at instantiation time.
Index: cfe/trunk/unittests/Tooling/ToolingTest.cpp
===================================================================
--- cfe/trunk/unittests/Tooling/ToolingTest.cpp
+++ cfe/trunk/unittests/Tooling/ToolingTest.cpp
@@ -564,5 +564,31 @@
 }
 #endif
 
+TEST(runToolOnCode, TestResetDiagnostics) {
+  // This is a tool that resets the diagnostic during the compilation.
+  struct ResetDiagnosticAction : public clang::ASTFrontendAction {
+    std::unique_ptr<ASTConsumer> CreateASTConsumer(CompilerInstance &Compiler,
+                                                   StringRef) override {
+      struct Consumer : public clang::ASTConsumer {
+        bool HandleTopLevelDecl(clang::DeclGroupRef D) override {
+          auto &Diags = (*D.begin())->getASTContext().getDiagnostics();
+          // Ignore any error
+          Diags.Reset();
+          // Disable warnings because computing the CFG might crash.
+          Diags.setIgnoreAllWarnings(true);
+          return true;
+        }
+      };
+      return llvm::make_unique<Consumer>();
+    }
+  };
+
+  // Should not crash
+  EXPECT_FALSE(
+      runToolOnCode(new ResetDiagnosticAction,
+                    "struct Foo { Foo(int); ~Foo(); struct Fwd _fwd; };"
+                    "void func() { long x; Foo f(x); }"));
+}
+
 } // end namespace tooling
 } // end namespace clang