feat(mol): spawn molecules as ephemeral by default (bd-2vh3.2)

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>

cmd/bd/mol.go

@@ -62,8 +62,9 @@ Commands:
 // spawnMolecule creates new issues from the proto with variable substitution.
 // This instantiates a proto (template) into a molecule (real issues).
 // Wraps cloneSubgraph from template.go and returns InstantiateResult.
-func spawnMolecule(ctx context.Context, s storage.Storage, subgraph *MoleculeSubgraph, vars map[string]string, assignee string, actorName string) (*InstantiateResult, error) {
-	return cloneSubgraph(ctx, s, subgraph, vars, assignee, actorName)
+// If ephemeral is true, spawned issues are marked for bulk deletion when closed.
+func spawnMolecule(ctx context.Context, s storage.Storage, subgraph *MoleculeSubgraph, vars map[string]string, assignee string, actorName string, ephemeral bool) (*InstantiateResult, error) {
+	return cloneSubgraph(ctx, s, subgraph, vars, assignee, actorName, ephemeral)
 }
 
 // printMoleculeTree prints the molecule structure as a tree