Explicitly apply mirror and auth settings to remote repos in the CLI

Previously, the CLI relied on Aether using the session's mirror
selector and authentication selector to customize the configured
repositories. These selectors are only used to configure what Aether
calls recessive repositories (repositories discovered when resolving
an artifact), rather than the explicitly configured repositories that
are typically used.

This commit updates AetherGrapeEngine to apply mirror and
authentication configuration to every added repository, bringing its
behaviour for these two settings into line with what it already does
for proxy configuration.

Fixes #1354