Fix Zeitwerk eager loading and GemfileHelper conflicts

[knu]

• Skip duplicate gems in GemfileHelper — Instead of aborting on gem version conflicts between the agent gemspec and huginn's Gemfile, silently skip gems that are already present. This avoids unnecessary failures when versions are compatible.
• Require registered agent files directly — Replace setup_zeitwerk_loader with plain require. The Zeitwerk loader mapped the entire lib/<gem_name>/ directory to the Agents namespace, which caused version.rb to be eagerly loaded as Agents::Version and fail with NameError in CI (eager_load = true).