Add --gastown flag to bd doctor for gastown-specific checks (#1162)

When running in gastown multi-workspace mode, two checks produce false
positives that are expected behavior:

1. routes.jsonl is a valid configuration file (maps issue prefixes to
   rig directories), not a duplicate JSONL file
2. Duplicate issues are expected (ephemeral wisps from patrol cycles)
   and normal up to ~1000, with GC cleaning them up automatically

This commit adds flags to bd doctor for gastown-specific checks:
- --gastown: Skip routes.jsonl warning and enable duplicate threshold
- --gastown-duplicates-threshold=N: Set duplicate tolerance (default 1000)

Fixes false positive warnings:
  Multiple JSONL files found: issues.jsonl, routes.jsonl
  70 duplicate issue(s) in 30 group(s)

Changes:
- Add --gastown flag to bd doctor command
- Add --gastown-duplicates-threshold flag (default: 1000)
- Update CheckLegacyJSONLFilename to skip routes.jsonl when gastown mode active
- Update CheckDuplicateIssues to use configurable threshold when gastown mode active
- Add test cases for gastown mode behavior with various thresholds

Co-authored-by: Roland Tritsch <roland@ailtir.com>
Co-authored-by: Claude Sonnet 4.5 <noreply@anthropic.com>

cmd/bd/doctor/legacy_test.go

@@ -209,96 +209,126 @@ func TestCheckLegacyJSONLFilename(t *testing.T) {
 	tests := []struct {
 		name           string
 		files          []string
+		gastownMode    bool
 		expectedStatus string
 		expectWarning  bool
 	}{
 		{
 			name:           "no JSONL files",
 			files:          []string{},
+			gastownMode:    false,
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
 		{
 			name:           "single issues.jsonl",
 			files:          []string{"issues.jsonl"},
+			gastownMode:    false,
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
 		{
 			name:           "single beads.jsonl is ok",
 			files:          []string{"beads.jsonl"},
+			gastownMode:    false,
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
 		{
 			name:           "custom name is ok",
 			files:          []string{"my-issues.jsonl"},
+			gastownMode:    false,
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
 		{
 			name:           "multiple JSONL files warning",
 			files:          []string{"beads.jsonl", "issues.jsonl"},
+			gastownMode:    false,
+			expectedStatus: "warning",
+			expectWarning:  true,
+		},
+		{
+			name:           "routes.jsonl with gastown flag",
+			files:          []string{"issues.jsonl", "routes.jsonl"},
+			gastownMode:    true,
+			expectedStatus: "ok",
+			expectWarning:  false,
+		},
+		{
+			name:           "routes.jsonl without gastown flag",
+			files:          []string{"issues.jsonl", "routes.jsonl"},
+			gastownMode:    false,
 			expectedStatus: "warning",
 			expectWarning:  true,
 		},
 		{
 			name:           "backup files ignored",
 			files:          []string{"issues.jsonl", "issues.jsonl.backup", "BACKUP_issues.jsonl"},
+			gastownMode:    false,
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
 		{
 			name:           "multiple real files with backups",
 			files:          []string{"issues.jsonl", "beads.jsonl", "issues.jsonl.backup"},
+			gastownMode:    false,
 			expectedStatus: "warning",
 			expectWarning:  true,
 		},
 		{
 			name:           "deletions.jsonl ignored as system file",
 			files:          []string{"beads.jsonl", "deletions.jsonl"},
+			gastownMode:    false,
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
 		{
 			name:           "merge artifacts ignored",
 			files:          []string{"issues.jsonl", "issues.base.jsonl", "issues.left.jsonl"},
+			gastownMode:    false,
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
 		{
 			name:           "merge artifacts with right variant ignored",
 			files:          []string{"issues.jsonl", "issues.right.jsonl"},
+			gastownMode:    false,
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
 		{
 			name:           "beads merge artifacts ignored (bd-ov1)",
 			files:          []string{"issues.jsonl", "beads.base.jsonl", "beads.left.jsonl"},
+			gastownMode:    false,
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
 		{
 			name:           "interactions.jsonl ignored as system file (GH#709)",
 			files:          []string{"issues.jsonl", "interactions.jsonl"},
+			gastownMode:    false,
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
 		{
 			name:           "molecules.jsonl ignored as system file",
 			files:          []string{"issues.jsonl", "molecules.jsonl"},
+			gastownMode:    false,
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
 		{
 			name:           "sync_base.jsonl ignored as system file (GH#1021)",
 			files:          []string{"issues.jsonl", "sync_base.jsonl"},
+			gastownMode:    false,
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
 		{
 			name:           "all system files ignored together",
 			files:          []string{"issues.jsonl", "deletions.jsonl", "interactions.jsonl", "molecules.jsonl", "sync_base.jsonl"},
+			gastownMode:    false,
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
@@ -320,7 +350,7 @@ func TestCheckLegacyJSONLFilename(t *testing.T) {
 				}
 			}
 
-			check := CheckLegacyJSONLFilename(tmpDir)
+			check := CheckLegacyJSONLFilename(tmpDir, tt.gastownMode)
 
 			if check.Status != tt.expectedStatus {
 				t.Errorf("Expected status %s, got %s", tt.expectedStatus, check.Status)