fix(doctor): exclude sync_base.jsonl from multiple JSONL files check (#1021)

sync_base.jsonl is an internal sync mechanism file used for 3-way merge,
not a competing issue database. The doctor check now correctly ignores it.

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

cmd/bd/doctor/legacy.go

@@ -156,6 +156,7 @@ func CheckLegacyJSONLFilename(repoPath string) DoctorCheck {
 			name == "deletions.jsonl" ||
 			name == "interactions.jsonl" ||
 			name == "molecules.jsonl" ||
+			name == "sync_base.jsonl" ||
 			// Git merge conflict artifacts (e.g., issues.base.jsonl, issues.left.jsonl)
 			strings.Contains(lowerName, ".base.jsonl") ||
 			strings.Contains(lowerName, ".left.jsonl") ||

cmd/bd/doctor/legacy_test.go

@@ -290,9 +290,15 @@ func TestCheckLegacyJSONLFilename(t *testing.T) {
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
+		{
+			name:           "sync_base.jsonl ignored as system file (GH#1021)",
+			files:          []string{"issues.jsonl", "sync_base.jsonl"},
+			expectedStatus: "ok",
+			expectWarning:  false,
+		},
 		{
 			name:           "all system files ignored together",
-			files:          []string{"issues.jsonl", "deletions.jsonl", "interactions.jsonl", "molecules.jsonl"},
+			files:          []string{"issues.jsonl", "deletions.jsonl", "interactions.jsonl", "molecules.jsonl", "sync_base.jsonl"},
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},