docs: Clarify gt mol vs bd mol command distinction
Update reference.md to explain the separation:
- bd mol: beads data operations (list, show, pour, wisp, bond)
- gt mol: agent operations (status, current, attach, burn, squash)
Key clarification: gt mol burn/squash operate on current agent's
attached molecule (auto-detected), while bd mol burn/squash take
explicit molecule IDs.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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