[lit] Flush stderr manually on Windows after printing messages

When run in a git bash terminal, sys.stderr isn't flushed implicitly
after printing each line. Manually flush it after each printout,
to avoid getting broken/misordered output.

A similar fix had been done in the old libcxx test config, committed
as part of 7e3ee09a / D28725; this
generalizes the fix, making it available in the new libcxx test
configs too, and for any other test that uses lit_config.note().

Differential Revision: https://reviews.llvm.org/D115761