refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

Split 6 files exceeding 800 lines by extracting cohesive function groups:

- show.go (1592→578): extracted show_thread.go, close.go, edit.go, update.go
- doctor.go (1295→690): extracted doctor_fix.go, doctor_health.go, doctor_pollution.go
- sync.go (1201→749): extracted sync_git.go
- compact.go (1199→775): extracted compact_tombstone.go, compact_rpc.go
- linear.go (1190→641): extracted linear_sync.go, linear_conflict.go
- main.go (1148→800): extracted main_help.go, main_errors.go, main_daemon.go

All files now under 800-line acceptance criteria.

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

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

cmd/bd/doctor_pollution.go

@@ -0,0 +1,154 @@
+package main
+
+import (
+	"fmt"
+	"os"
+	"strings"
+
+	"github.com/steveyegge/beads/internal/types"
+	"github.com/steveyegge/beads/internal/ui"
+)
+
+// runPollutionCheck runs detailed test pollution detection
+// This integrates the detect-pollution command functionality into doctor.
+func runPollutionCheck(path string, clean bool, yes bool) {
+	// Ensure we have a store initialized (uses direct mode, no daemon support yet)
+	if err := ensureDirectMode("pollution check requires direct mode"); err != nil {
+		fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+		os.Exit(1)
+	}
+
+	ctx := rootCtx
+
+	// Get all issues
+	allIssues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "Error fetching issues: %v\n", err)
+		os.Exit(1)
+	}
+
+	// Detect pollution (reuse detectTestPollution from detect_pollution.go)
+	polluted := detectTestPollution(allIssues)
+
+	if len(polluted) == 0 {
+		if !jsonOutput {
+			fmt.Println("No test pollution detected!")
+		} else {
+			outputJSON(map[string]interface{}{
+				"polluted_count": 0,
+				"issues":         []interface{}{},
+			})
+		}
+		return
+	}
+
+	// Categorize by confidence
+	highConfidence := []pollutionResult{}
+	mediumConfidence := []pollutionResult{}
+
+	for _, p := range polluted {
+		if p.score >= 0.9 {
+			highConfidence = append(highConfidence, p)
+		} else {
+			mediumConfidence = append(mediumConfidence, p)
+		}
+	}
+
+	if jsonOutput {
+		result := map[string]interface{}{
+			"polluted_count":    len(polluted),
+			"high_confidence":   len(highConfidence),
+			"medium_confidence": len(mediumConfidence),
+			"issues":            []map[string]interface{}{},
+		}
+
+		for _, p := range polluted {
+			result["issues"] = append(result["issues"].([]map[string]interface{}), map[string]interface{}{
+				"id":         p.issue.ID,
+				"title":      p.issue.Title,
+				"score":      p.score,
+				"reasons":    p.reasons,
+				"created_at": p.issue.CreatedAt,
+			})
+		}
+
+		outputJSON(result)
+		return
+	}
+
+	// Human-readable output
+	fmt.Printf("Found %d potential test issues:\n\n", len(polluted))
+
+	if len(highConfidence) > 0 {
+		fmt.Printf("High Confidence (score ≥ 0.9):\n")
+		for _, p := range highConfidence {
+			fmt.Printf("  %s: %q (score: %.2f)\n", p.issue.ID, p.issue.Title, p.score)
+			for _, reason := range p.reasons {
+				fmt.Printf("    - %s\n", reason)
+			}
+		}
+		fmt.Printf("  (Total: %d issues)\n\n", len(highConfidence))
+	}
+
+	if len(mediumConfidence) > 0 {
+		fmt.Printf("Medium Confidence (score 0.7-0.9):\n")
+		for _, p := range mediumConfidence {
+			fmt.Printf("  %s: %q (score: %.2f)\n", p.issue.ID, p.issue.Title, p.score)
+			for _, reason := range p.reasons {
+				fmt.Printf("    - %s\n", reason)
+			}
+		}
+		fmt.Printf("  (Total: %d issues)\n\n", len(mediumConfidence))
+	}
+
+	if !clean {
+		fmt.Printf("Run 'bd doctor --check=pollution --clean' to delete these issues (with confirmation).\n")
+		return
+	}
+
+	// Confirmation prompt
+	if !yes {
+		fmt.Printf("\nDelete %d test issues? [y/N] ", len(polluted))
+		var response string
+		_, _ = fmt.Scanln(&response)
+		if strings.ToLower(response) != "y" {
+			fmt.Println("Canceled.")
+			return
+		}
+	}
+
+	// Backup to JSONL before deleting
+	backupPath := ".beads/pollution-backup.jsonl"
+	if err := backupPollutedIssues(polluted, backupPath); err != nil {
+		fmt.Fprintf(os.Stderr, "Error backing up issues: %v\n", err)
+		os.Exit(1)
+	}
+	fmt.Printf("Backed up %d issues to %s\n", len(polluted), backupPath)
+
+	// Delete issues
+	fmt.Printf("\nDeleting %d issues...\n", len(polluted))
+	deleted := 0
+	for _, p := range polluted {
+		if err := deleteIssue(ctx, p.issue.ID); err != nil {
+			fmt.Fprintf(os.Stderr, "Error deleting %s: %v\n", p.issue.ID, err)
+			continue
+		}
+		deleted++
+	}
+
+	// Schedule auto-flush
+	markDirtyAndScheduleFlush()
+
+	fmt.Printf("%s Deleted %d test issues\n", ui.RenderPass("✓"), deleted)
+	fmt.Printf("\nCleanup complete. To restore, run: bd import %s\n", backupPath)
+}
+
+func init() {
+	rootCmd.AddCommand(doctorCmd)
+	doctorCmd.Flags().BoolVar(&perfMode, "perf", false, "Run performance diagnostics and generate CPU profile")
+	doctorCmd.Flags().BoolVar(&checkHealthMode, "check-health", false, "Quick health check for git hooks (silent on success)")
+	doctorCmd.Flags().StringVarP(&doctorOutput, "output", "o", "", "Export diagnostics to JSON file")
+	doctorCmd.Flags().StringVar(&doctorCheckFlag, "check", "", "Run specific check in detail (e.g., 'pollution')")
+	doctorCmd.Flags().BoolVar(&doctorClean, "clean", false, "For pollution check: delete detected test issues")
+	doctorCmd.Flags().BoolVar(&doctorDeep, "deep", false, "Validate full graph integrity")
+}