Update some [stale] sections (manually verified these are now expected)

Author: Guido van Rossum

test-data/unit/check-incremental.test

@@ -537,7 +537,7 @@ def func2() -> str:
     return "foo"
 
 [rechecked mod0, mod1, mod2]
-[stale mod2]
+[stale mod0, mod2]
 [out2]
 tmp/mod1.py:4: error: Incompatible return value type (got "str", expected "int")
 
@@ -1113,7 +1113,7 @@ val = "foo"
 
 [builtins fixtures/module_all.pyi]
 [rechecked main, c, c.submodule]
-[stale]
+[stale c]
 [out2]
 tmp/c/submodule.py:2: error: Incompatible types in assignment (expression has type "str", variable has type "int")
 tmp/main.py:7: error: "C" has no attribute "foo"
@@ -1347,7 +1347,7 @@ class C:
     def foo(self) -> int: return 1
 
 [rechecked mod3, mod2, mod1]
-[stale mod3, mod2]
+[stale mod3]
 [out1]
 tmp/mod3.py:5: error: Incompatible types in assignment (expression has type "str", variable has type "int")
 tmp/mod1.py:3: error: Revealed type is 'builtins.int'
@@ -1429,7 +1429,7 @@ class C:
     def foo(self) -> str: return 'a'
 
 [rechecked mod4, mod3, mod2, mod1]
-[stale mod4, mod3, mod2]
+[stale mod4, mod3]
 [out1]
 tmp/mod3.py:5: error: Incompatible types in assignment (expression has type "str", variable has type "int")
 tmp/mod1.py:3: error: Revealed type is 'builtins.int'
@@ -3435,14 +3435,21 @@ extra = 1
 
 [case testErrorsAffectDependentsOnly]
 # cmd: mypy -m m.a m.b m.c
+
 [file m/__init__.py]
+
 [file m/a.py]
 1 + ''  # Deliberate error
+
 [file m/b.py]
 import m.a  # Depends on module with error
+
 [file m/c.py]
 import m  # No error here
+
 [rechecked m.a, m.b]
+[stale]
+
 [out1]
 tmp/m/a.py:1: error: Unsupported operand types for + ("int" and "str")
 [out2]