fix: rename BondRef.ProtoID to SourceID for clarity (bd-ia3g)

The ProtoID field in BondRef was misleading as it could hold both proto
IDs (from proto+proto bonds) and molecule IDs (from mol+mol bonds).
Rename to SourceID with updated JSON tag to better reflect its purpose.

Changes:
- Rename BondRef.ProtoID to SourceID in types.go
- Update JSON tag from proto_id to source_id
- Update all usages in mol_bond.go and tests

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/mol_bond.go

@@ -317,8 +317,8 @@ func bondProtoProto(ctx context.Context, s storage.Storage, protoA, protoB *type
 			Priority:    minPriority(protoA.Priority, protoB.Priority),
 			IssueType:   types.TypeEpic,
 			BondedFrom: []types.BondRef{
-				{ProtoID: protoA.ID, BondType: bondType, BondPoint: ""},
-				{ProtoID: protoB.ID, BondType: bondType, BondPoint: ""},
+				{SourceID: protoA.ID, BondType: bondType, BondPoint: ""},
+				{SourceID: protoB.ID, BondType: bondType, BondPoint: ""},
 			},
 		}
 		if err := tx.CreateIssue(ctx, compound, actorName); err != nil {

internal/types/types.go

@@ -128,7 +128,7 @@ func (i *Issue) ComputeContentHash() string {
 
 	// Bonded molecules
 	for _, br := range i.BondedFrom {
-		w.str(br.ProtoID)
+		w.str(br.SourceID)
 		w.str(br.BondType)
 		w.str(br.BondPoint)
 	}
@@ -795,7 +795,7 @@ type EpicStatus struct {
 // When protos or molecules are bonded together, BondRefs record
 // which sources were combined and how they were attached.
 type BondRef struct {
-	ProtoID   string `json:"proto_id"`             // Source proto/molecule ID
+	SourceID  string `json:"source_id"`            // Source proto or molecule ID
 	BondType  string `json:"bond_type"`            // sequential, parallel, conditional
 	BondPoint string `json:"bond_point,omitempty"` // Attachment site (issue ID or empty for root)
 }

internal/types/types_test.go

@@ -464,12 +464,12 @@ func TestIssueCompoundHelpers(t *testing.T) {
 		t.Fatalf("expected nil constituents for non-compound issue")
 	}
 
-	bonded := &Issue{BondedFrom: []BondRef{{ProtoID: "proto-1", BondType: BondTypeSequential}}}
+	bonded := &Issue{BondedFrom: []BondRef{{SourceID: "proto-1", BondType: BondTypeSequential}}}
 	if !bonded.IsCompound() {
 		t.Fatalf("issue with bonded refs should be compound")
 	}
 	refs := bonded.GetConstituents()
-	if len(refs) != 1 || refs[0].ProtoID != "proto-1" {
+	if len(refs) != 1 || refs[0].SourceID != "proto-1" {
 		t.Fatalf("unexpected constituents: %#v", refs)
 	}
 }