Some warnings are not printed to stderr

[zivnevo]

e.g., when running the following cmdline:

nca --connectivity -r https://github.com/GoogleCloudPlatform/microservices-demo/tree/main/release

Warnings such as Warning: over-approximation analysis: ports is not yet supported inside ServiceEntry,ignoring this key are printed to stdout.

The reason is that the new NcaLogger can collect messages while it is muted, but it does not store the file destination of these messages. Hence, when NcaLogger.flush_messages() is called, all messages get printed to stdout, even if they were originally sent to stderr.

This currently causes the testing of Baseline Rules Verifier to fail with NCA versions >= 1.9.3.

[zivnevo]

Fixed