diff --git a/cmd/bd/doctor/legacy.go b/cmd/bd/doctor/legacy.go
index 74fe64a7..36c7e4c9 100644
--- a/cmd/bd/doctor/legacy.go
+++ b/cmd/bd/doctor/legacy.go
@@ -139,7 +139,11 @@ func CheckLegacyJSONLFilename(repoPath string) DoctorCheck {
 			strings.Contains(lowerName, ".bak") ||
 			strings.Contains(lowerName, "~") ||
 			strings.HasPrefix(lowerName, "backup_") ||
-			name == "deletions.jsonl" {
+			name == "deletions.jsonl" ||
+			// Git merge conflict artifacts (e.g., issues.base.jsonl, issues.left.jsonl)
+			strings.Contains(lowerName, ".base.jsonl") ||
+			strings.Contains(lowerName, ".left.jsonl") ||
+			strings.Contains(lowerName, ".right.jsonl") {
 			continue
 		}
 
diff --git a/cmd/bd/doctor/legacy_test.go b/cmd/bd/doctor/legacy_test.go
index fd429475..d1154c2d 100644
--- a/cmd/bd/doctor/legacy_test.go
+++ b/cmd/bd/doctor/legacy_test.go
@@ -231,6 +231,18 @@ func TestCheckLegacyJSONLFilename(t *testing.T) {
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
+		{
+			name:           "merge artifacts ignored",
+			files:          []string{"issues.jsonl", "issues.base.jsonl", "issues.left.jsonl"},
+			expectedStatus: "ok",
+			expectWarning:  false,
+		},
+		{
+			name:           "merge artifacts with right variant ignored",
+			files:          []string{"issues.jsonl", "issues.right.jsonl"},
+			expectedStatus: "ok",
+			expectWarning:  false,
+		},
 	}
 
 	for _, tt := range tests {