Fix ghc-pkg reports cache out date (#10205)

See Note [writeAtomic leaky abstraction].

GHC on Linux already received a patch for this bug in
e0801a0f. On Windows several cabal tests
were hitting the bug, causing validate failures, but we never noticed
because of all the other tests that were failing on Windows. And it
didn't start happening till `getModificationTime` received sub-second
resolution support on Windows in
5cf76186.

Since there are regression tests already, I am not adding another one.
But for good measure, here is a script that shows the bug without
needing to do a full validate run:

  DB=/tmp/package.conf.d.test
  GHC_PKG=ghc-pkg #utils/ghc-pkg/dist/build/tmp/ghc-pkg
  LOCAL_GHC_PKG="${GHC_PKG} --no-user-package-db --global-package-db=${DB}"
  while true; do
    rm -rf ${DB}
    ${LOCAL_GHC_PKG} init "${DB}"
    ${LOCAL_GHC_PKG} list
  done

If you see "WARNING: cache is out of date" after a few seconds, the bug
is not fixed.

Reviewed By: austin

Differential Revision: https://phabricator.haskell.org/D990

GHC Trac Issues: #10205