Rewrite all import statements, patch() targets, sys.modules keys,
importlib.import_module() strings, and subprocess -m references to use
hermes_agent.* paths.
Strip sys.path.insert hacks from production code (rely on editable install).
Update COMPONENT_PREFIXES for logger filtering.
Fix 3 hardcoded getLogger() calls to use __name__.
Update transport and tool registry discovery paths.
Update plugin module path strings.
Add legacy process-name patterns for gateway PID detection.
Add main() to skills_sync for console_script entry point.
Fix _get_bundled_dir() path traversal after move.
Part of #14182, #14183
Pure file moves, zero content changes. Every file in agent/, tools/,
hermes_cli/, gateway/, acp_adapter/, cron/, and plugins/ moves into
hermes_agent/. Top-level modules (run_agent.py, cli.py, etc.) move to
their new homes per the restructure manifest.
Git sees 100% similarity on all moves.
Part of #14182, #14183
