Incremental mode does extra work with --follow-imports=skip

[JukkaL]

In this case the warm run should do no work, since nothing changes:

[case testIncrementalFollowImportsSkipStubWithSkippedRuntimeDependency]
# flags: --follow-imports=skip
import pkg.foo
[file pkg/__init__.py]

[file pkg/foo.pyi]
from pkg import helper

x = 1
[file pkg/helper.py]
y = 2
[rechecked]
[stale]
[out2]
[out3]

However, pkg.foo is rechecked, which means mypy does redundant work:

________________ testIncrementalFollowImportsSkipStubWithSkippedRuntimeDependency _________________
data: /Users/jukka/src/alt-mypy/test-data/unit/check-incremental.test:4743:
Failed: Actual modules (pkg.foo) do not match expected modules () for "[rechecked ...]"
-------------------------------------- Captured stderr call ---------------------------------------
Expected:
Actual:
  pkg.foo (diff)

The second incremental run works as expected -- only the first warm run appears to do extra work.

[JukkaL]

cc @ilevkivskyi since you've worked on incremental checking recently (but this doesn't appear to be a recent regression)