diff --git a/cmd/bd/doctor/legacy.go b/cmd/bd/doctor/legacy.go
index 3f5112b9..589d3b9b 100644
--- a/cmd/bd/doctor/legacy.go
+++ b/cmd/bd/doctor/legacy.go
@@ -154,6 +154,8 @@ func CheckLegacyJSONLFilename(repoPath string) DoctorCheck {
 			strings.Contains(lowerName, "~") ||
 			strings.HasPrefix(lowerName, "backup_") ||
 			name == "deletions.jsonl" ||
+			name == "interactions.jsonl" ||
+			name == "molecules.jsonl" ||
 			// Git merge conflict artifacts (e.g., issues.base.jsonl, issues.left.jsonl)
 			strings.Contains(lowerName, ".base.jsonl") ||
 			strings.Contains(lowerName, ".left.jsonl") ||
diff --git a/cmd/bd/doctor/legacy_test.go b/cmd/bd/doctor/legacy_test.go
index bcd0bafd..241c9d75 100644
--- a/cmd/bd/doctor/legacy_test.go
+++ b/cmd/bd/doctor/legacy_test.go
@@ -278,6 +278,24 @@ func TestCheckLegacyJSONLFilename(t *testing.T) {
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
+		{
+			name:           "interactions.jsonl ignored as system file (GH#709)",
+			files:          []string{"issues.jsonl", "interactions.jsonl"},
+			expectedStatus: "ok",
+			expectWarning:  false,
+		},
+		{
+			name:           "molecules.jsonl ignored as system file",
+			files:          []string{"issues.jsonl", "molecules.jsonl"},
+			expectedStatus: "ok",
+			expectWarning:  false,
+		},
+		{
+			name:           "all system files ignored together",
+			files:          []string{"issues.jsonl", "deletions.jsonl", "interactions.jsonl", "molecules.jsonl"},
+			expectedStatus: "ok",
+			expectWarning:  false,
+		},
 	}
 
 	for _, tt := range tests {