diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
new file mode 100644
index 00000000000..d42fc1cd136
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "outputdir_module_multifolder/ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index b4be78a74af..d42fc1cd136 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -15,8 +15,8 @@ declare module "outputdir_module_multifolder_ref/m2" {
     export function m2_f1(): m2_c1;
 }
 declare module "test" {
-    import m1 = require("ref/m1");
-    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
     export var a1: number;
     export class c1 {
         p1: number;
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
new file mode 100644
index 00000000000..d42fc1cd136
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "outputdir_module_multifolder/ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index b4be78a74af..d42fc1cd136 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -15,8 +15,8 @@ declare module "outputdir_module_multifolder_ref/m2" {
     export function m2_f1(): m2_c1;
 }
 declare module "test" {
-    import m1 = require("ref/m1");
-    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
     export var a1: number;
     export class c1 {
         p1: number;
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
new file mode 100644
index 00000000000..d42fc1cd136
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "outputdir_module_multifolder/ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index b4be78a74af..d42fc1cd136 100644
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -15,8 +15,8 @@ declare module "outputdir_module_multifolder_ref/m2" {
     export function m2_f1(): m2_c1;
 }
 declare module "test" {
-    import m1 = require("ref/m1");
-    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
     export var a1: number;
     export class c1 {
         p1: number;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
new file mode 100644
index 00000000000..d42fc1cd136
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "outputdir_module_multifolder/ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index b4be78a74af..d42fc1cd136 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -15,8 +15,8 @@ declare module "outputdir_module_multifolder_ref/m2" {
     export function m2_f1(): m2_c1;
 }
 declare module "test" {
-    import m1 = require("ref/m1");
-    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
     export var a1: number;
     export class c1 {
         p1: number;
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
new file mode 100644
index 00000000000..d42fc1cd136
--- /dev/null
+++ b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "outputdir_module_multifolder/ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index b4be78a74af..d42fc1cd136 100644
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -15,8 +15,8 @@ declare module "outputdir_module_multifolder_ref/m2" {
     export function m2_f1(): m2_c1;
 }
 declare module "test" {
-    import m1 = require("ref/m1");
-    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
     export var a1: number;
     export class c1 {
         p1: number;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
new file mode 100644
index 00000000000..d42fc1cd136
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "outputdir_module_multifolder/ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index b4be78a74af..d42fc1cd136 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -15,8 +15,8 @@ declare module "outputdir_module_multifolder_ref/m2" {
     export function m2_f1(): m2_c1;
 }
 declare module "test" {
-    import m1 = require("ref/m1");
-    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
     export var a1: number;
     export class c1 {
         p1: number;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
new file mode 100644
index 00000000000..d42fc1cd136
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "outputdir_module_multifolder/ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index b4be78a74af..d42fc1cd136 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -15,8 +15,8 @@ declare module "outputdir_module_multifolder_ref/m2" {
     export function m2_f1(): m2_c1;
 }
 declare module "test" {
-    import m1 = require("ref/m1");
-    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
     export var a1: number;
     export class c1 {
         p1: number;
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
new file mode 100644
index 00000000000..d42fc1cd136
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "outputdir_module_multifolder/ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index b4be78a74af..d42fc1cd136 100644
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -15,8 +15,8 @@ declare module "outputdir_module_multifolder_ref/m2" {
     export function m2_f1(): m2_c1;
 }
 declare module "test" {
-    import m1 = require("ref/m1");
-    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
     export var a1: number;
     export class c1 {
         p1: number;
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
new file mode 100644
index 00000000000..d42fc1cd136
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "outputdir_module_multifolder/ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index b4be78a74af..d42fc1cd136 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -15,8 +15,8 @@ declare module "outputdir_module_multifolder_ref/m2" {
     export function m2_f1(): m2_c1;
 }
 declare module "test" {
-    import m1 = require("ref/m1");
-    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    import m1 = require("outputdir_module_multifolder/ref/m1");
+    import m2 = require("outputdir_module_multifolder_ref/m2");
     export var a1: number;
     export class c1 {
         p1: number;