Molecule spawning now creates ephemeral issues that can be bulk-deleted
when closed using `bd cleanup --ephemeral`. This supports the ephemeral
molecule workflow pattern where execution traces are cleaned up while
outcomes persist.
Changes:
- Add `ephemeral` parameter to cloneSubgraph() and spawnMolecule()
- mol spawn: ephemeral=true by default, add --persistent flag to opt out
- mol run: ephemeral=true (molecule execution)
- mol bond: ephemeral=true (bonded protos)
- template instantiate: ephemeral=false (deprecated, backwards compat)
This is Tier 1 of the ephemeral molecule workflow epic (bd-2vh3).
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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