diff --git a/clang/test/utils/update_cc_test_checks/Inputs/exec-all-runlines.c b/clang/test/utils/update_cc_test_checks/Inputs/exec-all-runlines.c
--- a/clang/test/utils/update_cc_test_checks/Inputs/exec-all-runlines.c
+++ b/clang/test/utils/update_cc_test_checks/Inputs/exec-all-runlines.c
@@ -1,6 +1,6 @@
 // Check that the non-clang/non-filechecked runlines execute
-// RUN: cp %s %S/Output/execute-all-runlines.copy.c
-// RUN: cp %S/Output/execute-all-runlines.copy.c %s.copy.c
+// RUN: cp %s %S/execute-all-runlines.copy.c
+// RUN: cp %S/execute-all-runlines.copy.c %s.copy.c
 // RUN: %clang_cc1 -triple x86_64-unknown-linux-gnu -fopenmp %s.copy.c -emit-llvm-bc -o %t-host.bc
 // RUN: %clang_cc1 -triple x86_64-unknown-linux-gnu -fopenmp -fopenmp-host-ir-file-path %t-host.bc %s.copy.c -emit-llvm -o - | FileCheck %s --check-prefix=CHECK1
 // RUN: %clang_cc1 -triple x86_64-unknown-linux-gnu -emit-pch %s -o %t
diff --git a/clang/test/utils/update_cc_test_checks/Inputs/exec-all-runlines.c.expected b/clang/test/utils/update_cc_test_checks/Inputs/exec-all-runlines.c.expected
--- a/clang/test/utils/update_cc_test_checks/Inputs/exec-all-runlines.c.expected
+++ b/clang/test/utils/update_cc_test_checks/Inputs/exec-all-runlines.c.expected
@@ -1,7 +1,7 @@
 // NOTE: Assertions have been autogenerated by utils/update_cc_test_checks.py
 // Check that the non-clang/non-filechecked runlines execute
-// RUN: cp %s %S/Output/execute-all-runlines.copy.c
-// RUN: cp %S/Output/execute-all-runlines.copy.c %s.copy.c
+// RUN: cp %s %S/execute-all-runlines.copy.c
+// RUN: cp %S/execute-all-runlines.copy.c %s.copy.c
 // RUN: %clang_cc1 -triple x86_64-unknown-linux-gnu -fopenmp %s.copy.c -emit-llvm-bc -o %t-host.bc
 // RUN: %clang_cc1 -triple x86_64-unknown-linux-gnu -fopenmp -fopenmp-host-ir-file-path %t-host.bc %s.copy.c -emit-llvm -o - | FileCheck %s --check-prefix=CHECK1
 // RUN: %clang_cc1 -triple x86_64-unknown-linux-gnu -emit-pch %s -o %t
diff --git a/llvm/utils/update_cc_test_checks.py b/llvm/utils/update_cc_test_checks.py
--- a/llvm/utils/update_cc_test_checks.py
+++ b/llvm/utils/update_cc_test_checks.py
@@ -238,11 +238,8 @@
     run_list = []
     line2func_list = collections.defaultdict(list)
 
-    subs = {
-      '%s' : ti.path,
-      '%t' : tempfile.NamedTemporaryFile().name,
-      '%S' : os.getcwd(),
-    }
+    subs = common.getSubstitutions(ti.path)
+    subs.append(('%t', tempfile.NamedTemporaryFile().name))
 
     for l in ti.run_lines:
       commands = [cmd.strip() for cmd in l.split('|')]
@@ -257,16 +254,14 @@
       # Execute non-clang runline.
       if exec_args[0] not in SUBST:
         # Do lit-like substitutions.
-        for s in subs:
-          exec_args = [i.replace(s, subs[s]) if s in i else i for i in exec_args]
+        exec_args = [common.applySubstitutions(a, subs) for a in exec_args]
         run_list.append((None, exec_args, None, None))
         continue
       # This is a clang runline, apply %clang substitution rule, do lit-like substitutions,
       # and append args.clang_args
       clang_args = exec_args
       clang_args[0:1] = SUBST[clang_args[0]]
-      for s in subs:
-        clang_args = [i.replace(s, subs[s]) if s in i else i for i in clang_args]
+      clang_args = [common.applySubstitutions(a, subs) for a in clang_args]
       clang_args += ti.args.clang_args
 
       # Extract -check-prefix in FileCheck args