Replace passthrough() + stdlib flag.FlagSet anti-pattern with proper
cobra integration. Every Run* function now takes a typed *Opts struct
and returns error. Flags registered via cli.StringFlag/IntFlag/etc.
Commands participate in Core lifecycle with full cobra flag parsing.
- 6 command groups: gen, score, data, export, infra, mon
- 25 commands converted, 0 passthrough() calls remain
- Delete passthrough() helper from lem.go
- Update export_test.go to use ExportOpts struct
Co-Authored-By: Virgil <virgil@lethean.io>
ReadScorerOutput error was silently discarded during resume merge,
risking partial data loss on TOCTOU file changes. Also clean up
compare command construction to pass RunE directly to NewCommand.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
All 28 commands now accessible as exported lem.Run* functions.
Prerequisite for CLI framework migration.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
