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>
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