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_bond.go

@@ -283,8 +283,8 @@ func bondProtoMol(ctx context.Context, s storage.Storage, proto, mol *types.Issu
 		return nil, fmt.Errorf("missing required variables: %s (use --var)", strings.Join(missingVars, ", "))
 	}
 
-	// Spawn the proto
-	spawnResult, err := spawnMolecule(ctx, s, subgraph, vars, "", actorName)
+	// Spawn the proto (ephemeral by default for molecule execution - bd-2vh3)
+	spawnResult, err := spawnMolecule(ctx, s, subgraph, vars, "", actorName, true)
 	if err != nil {
 		return nil, fmt.Errorf("spawning proto: %w", err)
 	}