fix(merge): preserve close_reason field during merge/sync (GH#891)

The close_reason and closed_by_session fields were being silently dropped
during 3-way merge operations because the simplified Issue struct in
internal/merge/merge.go was missing these fields.

Changes:
- Add CloseReason and ClosedBySession fields to merge.Issue struct
- Implement merge logic that preserves these fields when status is closed
- Use timestamp-based conflict resolution (later closed_at wins)
- Clear close metadata when status becomes non-closed

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

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

internal/merge/merge.go

@@ -48,10 +48,12 @@ type Issue struct {
 	Status       string       `json:"status,omitempty"`
 	Priority     int          `json:"priority"` // No omitempty: 0 is valid (P0/critical)
 	IssueType    string       `json:"issue_type,omitempty"`
-	CreatedAt    string       `json:"created_at,omitempty"`
+	CreatedAt       string       `json:"created_at,omitempty"`
-	UpdatedAt    string       `json:"updated_at,omitempty"`
+	UpdatedAt       string       `json:"updated_at,omitempty"`
-	ClosedAt     string       `json:"closed_at,omitempty"`
+	ClosedAt        string       `json:"closed_at,omitempty"`
-	CreatedBy    string       `json:"created_by,omitempty"`
+	CloseReason     string       `json:"close_reason,omitempty"`     // Reason provided when closing (GH#891)
+	ClosedBySession string       `json:"closed_by_session,omitempty"` // Session that closed this issue (GH#891)
+	CreatedBy       string       `json:"created_by,omitempty"`
 	Dependencies []Dependency `json:"dependencies,omitempty"`
 	RawLine      string       `json:"-"` // Store original line for conflict output
 	// Tombstone fields: inline soft-delete support for merge
@@ -596,8 +598,23 @@ func mergeIssue(base, left, right Issue) (Issue, string) {
 	// This prevents invalid state (status=open with closed_at set)
 	if result.Status == StatusClosed {
 		result.ClosedAt = maxTime(left.ClosedAt, right.ClosedAt)
+		// Merge close_reason and closed_by_session - use value from side with later closed_at (GH#891)
+		// This ensures we keep the most recent close action's metadata
+		if isTimeAfter(left.ClosedAt, right.ClosedAt) {
+			result.CloseReason = left.CloseReason
+			result.ClosedBySession = left.ClosedBySession
+		} else if right.ClosedAt != "" {
+			result.CloseReason = right.CloseReason
+			result.ClosedBySession = right.ClosedBySession
+		} else {
+			// Both empty or only left has value - prefer left
+			result.CloseReason = left.CloseReason
+			result.ClosedBySession = left.ClosedBySession
+		}
 	} else {
 		result.ClosedAt = ""
+		result.CloseReason = ""
+		result.ClosedBySession = ""
 	}
 
 	// Merge dependencies - proper 3-way merge where removals win

internal/merge/merge_test.go

@@ -2460,3 +2460,265 @@ func TestMerge3Way_DeterministicOutputOrder(t *testing.T) {
 		}
 	})
 }
+// TestMerge3Way_CloseReasonPreservation tests that close_reason and closed_by_session
+// are preserved during merge/sync operations (GH#891)
+func TestMerge3Way_CloseReasonPreservation(t *testing.T) {
+	t.Run("close_reason preserved when both sides closed - later closed_at wins", func(t *testing.T) {
+		base := []Issue{
+			{
+				ID:        "bd-close1",
+				Title:     "Test Issue",
+				Status:    "open",
+				CreatedAt: "2024-01-01T00:00:00Z",
+				CreatedBy: "user1",
+			},
+		}
+		left := []Issue{
+			{
+				ID:              "bd-close1",
+				Title:           "Test Issue",
+				Status:          "closed",
+				ClosedAt:        "2024-01-02T00:00:00Z", // Earlier
+				CloseReason:     "Fixed in commit abc",
+				ClosedBySession: "session-left",
+				CreatedAt:       "2024-01-01T00:00:00Z",
+				CreatedBy:       "user1",
+			},
+		}
+		right := []Issue{
+			{
+				ID:              "bd-close1",
+				Title:           "Test Issue",
+				Status:          "closed",
+				ClosedAt:        "2024-01-03T00:00:00Z", // Later - should win
+				CloseReason:     "Fixed in commit xyz",
+				ClosedBySession: "session-right",
+				CreatedAt:       "2024-01-01T00:00:00Z",
+				CreatedBy:       "user1",
+			},
+		}
+
+		result, conflicts := merge3Way(base, left, right, false)
+		if len(conflicts) != 0 {
+			t.Errorf("expected no conflicts, got %d", len(conflicts))
+		}
+		if len(result) != 1 {
+			t.Fatalf("expected 1 merged issue, got %d", len(result))
+		}
+		// Right has later closed_at, so right's close_reason should win
+		if result[0].CloseReason != "Fixed in commit xyz" {
+			t.Errorf("expected close_reason 'Fixed in commit xyz', got %q", result[0].CloseReason)
+		}
+		if result[0].ClosedBySession != "session-right" {
+			t.Errorf("expected closed_by_session 'session-right', got %q", result[0].ClosedBySession)
+		}
+	})
+
+	t.Run("close_reason preserved when left has later closed_at", func(t *testing.T) {
+		base := []Issue{
+			{
+				ID:        "bd-close2",
+				Title:     "Test Issue",
+				Status:    "open",
+				CreatedAt: "2024-01-01T00:00:00Z",
+				CreatedBy: "user1",
+			},
+		}
+		left := []Issue{
+			{
+				ID:              "bd-close2",
+				Title:           "Test Issue",
+				Status:          "closed",
+				ClosedAt:        "2024-01-03T00:00:00Z", // Later - should win
+				CloseReason:     "Resolved by PR #123",
+				ClosedBySession: "session-left",
+				CreatedAt:       "2024-01-01T00:00:00Z",
+				CreatedBy:       "user1",
+			},
+		}
+		right := []Issue{
+			{
+				ID:              "bd-close2",
+				Title:           "Test Issue",
+				Status:          "closed",
+				ClosedAt:        "2024-01-02T00:00:00Z", // Earlier
+				CloseReason:     "Duplicate",
+				ClosedBySession: "session-right",
+				CreatedAt:       "2024-01-01T00:00:00Z",
+				CreatedBy:       "user1",
+			},
+		}
+
+		result, conflicts := merge3Way(base, left, right, false)
+		if len(conflicts) != 0 {
+			t.Errorf("expected no conflicts, got %d", len(conflicts))
+		}
+		if len(result) != 1 {
+			t.Fatalf("expected 1 merged issue, got %d", len(result))
+		}
+		// Left has later closed_at, so left's close_reason should win
+		if result[0].CloseReason != "Resolved by PR #123" {
+			t.Errorf("expected close_reason 'Resolved by PR #123', got %q", result[0].CloseReason)
+		}
+		if result[0].ClosedBySession != "session-left" {
+			t.Errorf("expected closed_by_session 'session-left', got %q", result[0].ClosedBySession)
+		}
+	})
+
+	t.Run("close_reason cleared when status becomes open", func(t *testing.T) {
+		base := []Issue{
+			{
+				ID:              "bd-close3",
+				Title:           "Test Issue",
+				Status:          "closed",
+				ClosedAt:        "2024-01-02T00:00:00Z",
+				CloseReason:     "Fixed",
+				ClosedBySession: "session-old",
+				CreatedAt:       "2024-01-01T00:00:00Z",
+				CreatedBy:       "user1",
+			},
+		}
+		left := []Issue{
+			{
+				ID:              "bd-close3",
+				Title:           "Test Issue",
+				Status:          "open", // Reopened
+				ClosedAt:        "",
+				CloseReason:     "", // Should be cleared
+				ClosedBySession: "",
+				CreatedAt:       "2024-01-01T00:00:00Z",
+				CreatedBy:       "user1",
+			},
+		}
+		right := []Issue{
+			{
+				ID:              "bd-close3",
+				Title:           "Test Issue",
+				Status:          "open", // Both reopened
+				ClosedAt:        "",
+				CloseReason:     "",
+				ClosedBySession: "",
+				CreatedAt:       "2024-01-01T00:00:00Z",
+				CreatedBy:       "user1",
+			},
+		}
+
+		result, conflicts := merge3Way(base, left, right, false)
+		if len(conflicts) != 0 {
+			t.Errorf("expected no conflicts, got %d", len(conflicts))
+		}
+		if len(result) != 1 {
+			t.Fatalf("expected 1 merged issue, got %d", len(result))
+		}
+		if result[0].Status != "open" {
+			t.Errorf("expected status 'open', got %q", result[0].Status)
+		}
+		if result[0].CloseReason != "" {
+			t.Errorf("expected empty close_reason when reopened, got %q", result[0].CloseReason)
+		}
+		if result[0].ClosedBySession != "" {
+			t.Errorf("expected empty closed_by_session when reopened, got %q", result[0].ClosedBySession)
+		}
+	})
+
+	t.Run("close_reason from single side preserved", func(t *testing.T) {
+		base := []Issue{
+			{
+				ID:        "bd-close4",
+				Title:     "Test Issue",
+				Status:    "open",
+				CreatedAt: "2024-01-01T00:00:00Z",
+				CreatedBy: "user1",
+			},
+		}
+		left := []Issue{
+			{
+				ID:              "bd-close4",
+				Title:           "Test Issue",
+				Status:          "closed",
+				ClosedAt:        "2024-01-02T00:00:00Z",
+				CloseReason:     "Won't fix - by design",
+				ClosedBySession: "session-abc",
+				CreatedAt:       "2024-01-01T00:00:00Z",
+				CreatedBy:       "user1",
+			},
+		}
+		right := []Issue{
+			{
+				ID:        "bd-close4",
+				Title:     "Test Issue",
+				Status:    "open", // Still open on right
+				CreatedAt: "2024-01-01T00:00:00Z",
+				CreatedBy: "user1",
+			},
+		}
+
+		result, conflicts := merge3Way(base, left, right, false)
+		if len(conflicts) != 0 {
+			t.Errorf("expected no conflicts, got %d", len(conflicts))
+		}
+		if len(result) != 1 {
+			t.Fatalf("expected 1 merged issue, got %d", len(result))
+		}
+		// Closed wins over open
+		if result[0].Status != "closed" {
+			t.Errorf("expected status 'closed', got %q", result[0].Status)
+		}
+		// Close reason from the closed side should be preserved
+		if result[0].CloseReason != "Won't fix - by design" {
+			t.Errorf("expected close_reason 'Won't fix - by design', got %q", result[0].CloseReason)
+		}
+		if result[0].ClosedBySession != "session-abc" {
+			t.Errorf("expected closed_by_session 'session-abc', got %q", result[0].ClosedBySession)
+		}
+	})
+
+	t.Run("close_reason survives round-trip through JSONL", func(t *testing.T) {
+		// This tests the full merge pipeline including JSON marshaling/unmarshaling
+		tmpDir := t.TempDir()
+
+		baseContent := `{"id":"bd-jsonl1","title":"Test Issue","status":"open","created_at":"2024-01-01T00:00:00Z","created_by":"user1"}`
+		leftContent := `{"id":"bd-jsonl1","title":"Test Issue","status":"closed","closed_at":"2024-01-02T00:00:00Z","close_reason":"Fixed in commit def456","closed_by_session":"session-jsonl","created_at":"2024-01-01T00:00:00Z","created_by":"user1"}`
+		rightContent := `{"id":"bd-jsonl1","title":"Test Issue","status":"open","created_at":"2024-01-01T00:00:00Z","created_by":"user1"}`
+
+		basePath := filepath.Join(tmpDir, "base.jsonl")
+		leftPath := filepath.Join(tmpDir, "left.jsonl")
+		rightPath := filepath.Join(tmpDir, "right.jsonl")
+		outputPath := filepath.Join(tmpDir, "output.jsonl")
+
+		if err := os.WriteFile(basePath, []byte(baseContent+"\n"), 0644); err != nil {
+			t.Fatal(err)
+		}
+		if err := os.WriteFile(leftPath, []byte(leftContent+"\n"), 0644); err != nil {
+			t.Fatal(err)
+		}
+		if err := os.WriteFile(rightPath, []byte(rightContent+"\n"), 0644); err != nil {
+			t.Fatal(err)
+		}
+
+		if err := Merge3Way(outputPath, basePath, leftPath, rightPath, false); err != nil {
+			t.Fatalf("Merge3Way failed: %v", err)
+		}
+
+		// Read output and verify close_reason is preserved
+		outputData, err := os.ReadFile(outputPath)
+		if err != nil {
+			t.Fatal(err)
+		}
+
+		var outputIssue Issue
+		if err := json.Unmarshal(outputData[:len(outputData)-1], &outputIssue); err != nil {
+			t.Fatalf("failed to parse output: %v", err)
+		}
+
+		if outputIssue.Status != "closed" {
+			t.Errorf("expected status 'closed', got %q", outputIssue.Status)
+		}
+		if outputIssue.CloseReason != "Fixed in commit def456" {
+			t.Errorf("expected close_reason 'Fixed in commit def456', got %q", outputIssue.CloseReason)
+		}
+		if outputIssue.ClosedBySession != "session-jsonl" {
+			t.Errorf("expected closed_by_session 'session-jsonl', got %q", outputIssue.ClosedBySession)
+		}
+	})
+}