FORGE-1133 Display warnings for errors in full project builds.

This displays warnings in the Shell for collection and resolution
errors in the full project build. It also displays warnings for
problems found in the Maven project model.
FORGE-1134 Fixing resolution failures for secured repositories

If a repository is defined along with a server configuration
element in settings.xml, then any username and password settings
configured, are used for that repository. Additionally, any
activeByDefault profiles are treated as active profiles with
this fix.

Passwords for mirrored repositories are determined at runtime
after Maven+Aether has performed a merge of the Maven model to
determine whether a mirror should used. The password for the
mirror is then retrieved at runtime if a mirror is involved.

Also fixed tests for ShellMessages failures. Delayed the
invocation of System.gc until all temp directories are deleted,
to improve build performance.