diff --git a/binary/proto_test.js b/binary/proto_test.js
index aee327a..1ece6b3 100644
--- a/binary/proto_test.js
+++ b/binary/proto_test.js
@@ -35,7 +35,7 @@ goog.require('goog.testing.asserts');
 goog.require('jspb.BinaryWriter');
 goog.require('jspb.Message');
 
-// CommonJS-LoadFromFile: ../testbinary_pb proto.jspb.test
+// CommonJS-LoadFromFile: ../protos/testbinary_pb proto.jspb.test
 goog.require('proto.jspb.test.ExtendsWithMessage');
 goog.require('proto.jspb.test.ForeignEnum');
 goog.require('proto.jspb.test.ForeignMessage');
diff --git a/commonjs/strict_test.js b/commonjs/strict_test.js
index 46458c1..58c8fce 100644
--- a/commonjs/strict_test.js
+++ b/commonjs/strict_test.js
@@ -39,8 +39,8 @@ var global = Function('return this')();
 // Bring asserts into the global namespace.
 googleProtobuf.object.extend(global, asserts);
 
-var test9_pb = require('./test9_pb');
-var test10_pb = require('./test10_pb');
+var test9_pb = require('./protos/test9_pb');
+var test10_pb = require('./protos/test10_pb');
 
 describe('Strict test suite', function() {
   it('testImportedMessage', function() {
diff --git a/gulpfile.js b/gulpfile.js
index 8cc8c31..0bc44f1 100644
--- a/gulpfile.js
+++ b/gulpfile.js
@@ -29,32 +29,32 @@ var wellKnownTypes = [
 wellKnownTypes.forEach((path, i) => protocInc + '/' + path);
 
 var group1Protos = [
-  'data.proto',
-  'test3.proto',
-  'test5.proto',
+  'protos/data.proto',
+  'protos/test3.proto',
+  'protos/test5.proto',
   'commonjs/test6/test6.proto',
-  'test8.proto',
-  'test11.proto',
-  'test12.proto',
-  'test13.proto',
-  'test14.proto',
-  'test15.proto',
-  'testbinary.proto',
-  'testempty.proto',
-  'test.proto',
-  'testlargenumbers.proto',
+  'protos/test8.proto',
+  'protos/test11.proto',
+  'protos/test12.proto',
+  'protos/test13.proto',
+  'protos/test14.proto',
+  'protos/test15.proto',
+  'protos/testbinary.proto',
+  'protos/testempty.proto',
+  'protos/test.proto',
+  'protos/testlargenumbers.proto',
 ];
 
 var group2Protos = [
-  'proto3_test.proto',
-  'test2.proto',
-  'test4.proto',
+  'protos/proto3_test.proto',
+  'protos/test2.proto',
+  'protos/test4.proto',
   'commonjs/test7/test7.proto',
 ];
 
 var group3Protos = [
-  'test9.proto',
-  'test10.proto'
+  'protos/test9.proto',
+  'protos/test10.proto'
 ];
 
 function make_exec_logging_callback(cb) {
diff --git a/maps_test.js b/maps_test.js
index 68ed683..718a350 100644
--- a/maps_test.js
+++ b/maps_test.js
@@ -31,7 +31,7 @@
 goog.require('goog.testing.asserts');
 goog.require('goog.userAgent');
 
-// CommonJS-LoadFromFile: testbinary_pb proto.jspb.test
+// CommonJS-LoadFromFile: protos/testbinary_pb proto.jspb.test
 goog.require('proto.jspb.test.MapValueEnum');
 goog.require('proto.jspb.test.MapValueMessage');
 goog.require('proto.jspb.test.TestMapFields');
@@ -49,7 +49,7 @@ goog.require('proto.jspb.test.MapEntryOptionalValuesDoubleValue');
 goog.require('proto.jspb.test.MapEntryOptionalValuesEnumValue');
 goog.require('proto.jspb.test.MapEntryOptionalValuesMessageValue');
 
-// CommonJS-LoadFromFile: test_pb proto.jspb.test
+// CommonJS-LoadFromFile: protos/test_pb proto.jspb.test
 goog.require('proto.jspb.test.MapValueMessageNoBinary');
 goog.require('proto.jspb.test.TestMapFieldsNoBinary');
 
diff --git a/message_test.js b/message_test.js
index 2a524de..5eb327e 100644
--- a/message_test.js
+++ b/message_test.js
@@ -36,20 +36,20 @@ goog.require('goog.testing.PropertyReplacer');
 goog.require('goog.testing.asserts');
 goog.require('goog.userAgent');
 
-// CommonJS-LoadFromFile: google-protobuf jspb
+// CommonJS-LoadFromFile: protos/google-protobuf jspb
 goog.require('jspb.Message');
 
-// CommonJS-LoadFromFile: test15_pb proto.jspb.filenametest.package1
+// CommonJS-LoadFromFile: protos/test15_pb proto.jspb.filenametest.package1
 goog.require('proto.jspb.filenametest.package1.b');
 
-// CommonJS-LoadFromFile: test14_pb proto.jspb.filenametest.package2
+// CommonJS-LoadFromFile: protos/test14_pb proto.jspb.filenametest.package2
 goog.require('proto.jspb.filenametest.package2.TestMessage');
 
-// CommonJS-LoadFromFile: test13_pb proto.jspb.filenametest.package1
+// CommonJS-LoadFromFile: protos/test13_pb proto.jspb.filenametest.package1
 goog.require('proto.jspb.filenametest.package1.a');
 goog.require('proto.jspb.filenametest.package1.TestMessage');
 
-// CommonJS-LoadFromFile: test12_pb proto.jspb.circulartest
+// CommonJS-LoadFromFile: protos/test12_pb proto.jspb.circulartest
 goog.require('proto.jspb.circulartest.ExtensionContainingType1');
 goog.require('proto.jspb.circulartest.ExtensionContainingType2');
 goog.require('proto.jspb.circulartest.ExtensionField1');
@@ -66,25 +66,25 @@ goog.require('proto.jspb.circulartest.NestedMessage2');
 goog.require('proto.jspb.circulartest.RepeatedMessageField1');
 goog.require('proto.jspb.circulartest.RepeatedMessageField2');
 
-// CommonJS-LoadFromFile: test11_pb proto.jspb.exttest.reverse
+// CommonJS-LoadFromFile: protos/test11_pb proto.jspb.exttest.reverse
 goog.require('proto.jspb.exttest.reverse.TestExtensionReverseOrderMessage1');
 goog.require('proto.jspb.exttest.reverse.TestExtensionReverseOrderMessage2');
 goog.require('proto.jspb.exttest.reverse.c');
 
-// CommonJS-LoadFromFile: test8_pb proto.jspb.exttest.nested
+// CommonJS-LoadFromFile: protos/test8_pb proto.jspb.exttest.nested
 goog.require('proto.jspb.exttest.nested.TestNestedExtensionsMessage');
 goog.require('proto.jspb.exttest.nested.TestOuterMessage');
 
-// CommonJS-LoadFromFile: test5_pb proto.jspb.exttest.beta
+// CommonJS-LoadFromFile: protos/test5_pb proto.jspb.exttest.beta
 goog.require('proto.jspb.exttest.beta.floatingStrField');
 
-// CommonJS-LoadFromFile: test3_pb proto.jspb.exttest
+// CommonJS-LoadFromFile: protos/test3_pb proto.jspb.exttest
 goog.require('proto.jspb.exttest.floatingMsgField');
 
-// CommonJS-LoadFromFile: test4_pb proto.jspb.exttest
+// CommonJS-LoadFromFile: protos/test4_pb proto.jspb.exttest
 goog.require('proto.jspb.exttest.floatingMsgFieldTwo');
 
-// CommonJS-LoadFromFile: test_pb proto.jspb.test
+// CommonJS-LoadFromFile: protos/test_pb proto.jspb.test
 goog.require('proto.jspb.test.BooleanFields');
 goog.require('proto.jspb.test.CloneExtension');
 goog.require('proto.jspb.test.Complex');
@@ -113,12 +113,12 @@ goog.require('proto.jspb.test.TestMessageWithOneof');
 goog.require('proto.jspb.test.TestReservedNames');
 goog.require('proto.jspb.test.TestReservedNamesExtension');
 
-// CommonJS-LoadFromFile: test2_pb proto.jspb.test
+// CommonJS-LoadFromFile: protos/test2_pb proto.jspb.test
 goog.require('proto.jspb.test.ExtensionMessage');
 goog.require('proto.jspb.test.TestExtensionsMessage');
 
 goog.require('proto.jspb.test.TestAllowAliasEnum');
-// CommonJS-LoadFromFile: testlargenumbers_pb proto.jspb.test
+// CommonJS-LoadFromFile: protos/testlargenumbers_pb proto.jspb.test
 goog.require('proto.jspb.test.MessageWithLargeFieldNumbers');
 
 goog.require('proto.jspb.test.simple1');
diff --git a/proto3_test.js b/proto3_test.js
index 8de1575..79b3205 100644
--- a/proto3_test.js
+++ b/proto3_test.js
@@ -30,9 +30,9 @@
 
 goog.require('goog.crypt.base64');
 goog.require('goog.testing.asserts');
-// CommonJS-LoadFromFile: testbinary_pb proto.jspb.test
+// CommonJS-LoadFromFile: protos/testbinary_pb proto.jspb.test
 goog.require('proto.jspb.test.ForeignMessage');
-// CommonJS-LoadFromFile: proto3_test_pb proto.jspb.test
+// CommonJS-LoadFromFile: protos/proto3_test_pb proto.jspb.test
 goog.require('proto.jspb.test.Proto3Enum');
 goog.require('proto.jspb.test.TestProto3');
 // CommonJS-LoadFromFile: google/protobuf/any_pb proto.google.protobuf
diff --git a/data.proto b/protos/data.proto
similarity index 100%
rename from data.proto
rename to protos/data.proto
diff --git a/proto3_test.proto b/protos/proto3_test.proto
similarity index 99%
rename from proto3_test.proto
rename to protos/proto3_test.proto
index 14f104e..81637ad 100644
--- a/proto3_test.proto
+++ b/protos/proto3_test.proto
@@ -32,7 +32,7 @@ syntax = "proto3";
 
 package jspb.test;
 
-import "testbinary.proto";
+import "protos/testbinary.proto";
 
 message TestProto3 {
   int32 singular_int32 = 1;
diff --git a/test.proto b/protos/test.proto
similarity index 100%
rename from test.proto
rename to protos/test.proto
diff --git a/test10.proto b/protos/test10.proto
similarity index 98%
rename from test10.proto
rename to protos/test10.proto
index 9fa5256..e9a1c16 100644
--- a/test10.proto
+++ b/protos/test10.proto
@@ -32,7 +32,7 @@ syntax = "proto3";
 
 package jspb.exttest.strict.ten;
 
-import "test9.proto";
+import "protos/test9.proto";
 
 message Simple10 {
     jspb.exttest.strict.nine.Simple9 a = 1;
diff --git a/test11.proto b/protos/test11.proto
similarity index 100%
rename from test11.proto
rename to protos/test11.proto
diff --git a/test12.proto b/protos/test12.proto
similarity index 100%
rename from test12.proto
rename to protos/test12.proto
diff --git a/test13.proto b/protos/test13.proto
similarity index 100%
rename from test13.proto
rename to protos/test13.proto
diff --git a/test14.proto b/protos/test14.proto
similarity index 100%
rename from test14.proto
rename to protos/test14.proto
diff --git a/test15.proto b/protos/test15.proto
similarity index 98%
rename from test15.proto
rename to protos/test15.proto
index b481116..c1f1caf 100644
--- a/test15.proto
+++ b/protos/test15.proto
@@ -32,7 +32,7 @@ syntax = "proto2";
 
 package jspb.filenametest.package1;
 
-import "test13.proto";
+import "protos/test13.proto";
 
 extend TestMessage {
   optional int32 b = 2;
diff --git a/test2.proto b/protos/test2.proto
similarity index 98%
rename from test2.proto
rename to protos/test2.proto
index e9457e7..0385157 100644
--- a/test2.proto
+++ b/protos/test2.proto
@@ -32,7 +32,7 @@ syntax = "proto2";
 
 package jspb.test;
 
-import "test.proto";
+import "protos/test.proto";
 
 option java_package = "com.google.apps.jspb.proto";
 option java_multiple_files = true;
diff --git a/test3.proto b/protos/test3.proto
similarity index 100%
rename from test3.proto
rename to protos/test3.proto
diff --git a/test4.proto b/protos/test4.proto
similarity index 98%
rename from test4.proto
rename to protos/test4.proto
index c3c8342..b40cc0a 100644
--- a/test4.proto
+++ b/protos/test4.proto
@@ -32,7 +32,7 @@ syntax = "proto2";
 
 package jspb.exttest;
 
-import "test3.proto";
+import "protos/test3.proto";
 
 option java_package = "com.google.apps.jspb.proto";
 option java_multiple_files = true;
diff --git a/test5.proto b/protos/test5.proto
similarity index 100%
rename from test5.proto
rename to protos/test5.proto
diff --git a/test8.proto b/protos/test8.proto
similarity index 100%
rename from test8.proto
rename to protos/test8.proto
diff --git a/test9.proto b/protos/test9.proto
similarity index 100%
rename from test9.proto
rename to protos/test9.proto
diff --git a/testbinary.proto b/protos/testbinary.proto
similarity index 100%
rename from testbinary.proto
rename to protos/testbinary.proto
diff --git a/testempty.proto b/protos/testempty.proto
similarity index 100%
rename from testempty.proto
rename to protos/testempty.proto
diff --git a/testlargenumbers.proto b/protos/testlargenumbers.proto
similarity index 100%
rename from testlargenumbers.proto
rename to protos/testlargenumbers.proto