Switch to use -m syntax instead of file syntax

Author: nipunn1313

test-data/unit/fine-grained-modules.test

@@ -903,9 +903,9 @@ main:2: error: Cannot find implementation or library stub for module named "p"
 
 [case testDeletePackage5]
 # flags: --namespace-packages
-# cmd1: mypy main p/a.py p/__init__.py
-# cmd2: mypy main p/a.py
-# cmd3: mypy main
+# cmd1: mypy -m main -m p.a -m p.__init__
+# cmd2: mypy -m main -m p.a
+# cmd3: mypy -m main
 
 import p.a
 p.a.f(1)
@@ -927,9 +927,9 @@ main:6: error: Cannot find implementation or library stub for module named "p"
 
 [case testDeletePackage6]
 # flags: --namespace-packages
-# cmd1: mypy p/a.py p/b.py p/__init__.py
-# cmd2: mypy p/a.py p/b.py
-# cmd3: mypy p/a.py p/b.py
+# cmd1: mypy -m p.a -m p.b -m p.__init__
+# cmd2: mypy -m p.a -m p.b
+# cmd3: mypy -m p.a -m p.b
 [file p/a.py]
 def f(x: str) -> None: pass
 [file p/b.py]