Add agents repo index and agents repo status CLI commands. The repo
index command triggers full or incremental indexing of a repository
resource. The status command displays indexing metadata including
file count, token estimate, primary language, and status. Both
commands support text and JSON output formats. Wires the existing
RepoIndexingService backend to the CLI layer.
Also fixes pre-existing test failures discovered during full nox
suite verification.
ISSUES CLOSED: #856