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>
2025-12-28 18:04:52 -08:00
parent 7ea7aee411
commit 6c14fd2225
22 changed files with 4251 additions and 4087 deletions
--- a/cmd/bd/doctor.go
+++ b/cmd/bd/doctor.go
@@ -1,25 +1,17 @@
 package main

 import (
-	"bufio"
-	"database/sql"
 	"encoding/json"
 	"fmt"
 	"os"
 	"path/filepath"
 	"slices"
-	"strings"
 	"time"

 	_ "github.com/ncruces/go-sqlite3/driver"
 	_ "github.com/ncruces/go-sqlite3/embed"
 	"github.com/spf13/cobra"
 	"github.com/steveyegge/beads/cmd/bd/doctor"
-	"github.com/steveyegge/beads/cmd/bd/doctor/fix"
-	"github.com/steveyegge/beads/internal/beads"
-	"github.com/steveyegge/beads/internal/configfile"
-	"github.com/steveyegge/beads/internal/syncbranch"
-	"github.com/steveyegge/beads/internal/types"
 	"github.com/steveyegge/beads/internal/ui"
 )

@@ -227,460 +219,6 @@ func init() {
 	doctorCmd.Flags().BoolVar(&doctorFixChildParent, "fix-child-parent", false, "Remove child→parent dependencies (opt-in)")
 }

-// previewFixes shows what would be fixed without applying changes
-func previewFixes(result doctorResult) {
-	// Collect all fixable issues
-	var fixableIssues []doctorCheck
-	for _, check := range result.Checks {
-		if (check.Status == statusWarning || check.Status == statusError) && check.Fix != "" {
-			fixableIssues = append(fixableIssues, check)
-		}
-	}
-
-	if len(fixableIssues) == 0 {
-		fmt.Println("\n✓ No fixable issues found (dry-run)")
-		return
-	}
-
-	fmt.Println("\n[DRY-RUN] The following issues would be fixed with --fix:")
-	fmt.Println()
-
-	for i, issue := range fixableIssues {
-		// Show the issue details
-		fmt.Printf("  %d. %s\n", i+1, issue.Name)
-		if issue.Status == statusError {
-			fmt.Printf("     Status: %s\n", ui.RenderFail("ERROR"))
-		} else {
-			fmt.Printf("     Status: %s\n", ui.RenderWarn("WARNING"))
-		}
-		fmt.Printf("     Issue:  %s\n", issue.Message)
-		if issue.Detail != "" {
-			fmt.Printf("     Detail: %s\n", issue.Detail)
-		}
-		fmt.Printf("     Fix:    %s\n", issue.Fix)
-		fmt.Println()
-	}
-
-	fmt.Printf("[DRY-RUN] Would attempt to fix %d issue(s)\n", len(fixableIssues))
-	fmt.Println("Run 'bd doctor --fix' to apply these fixes")
-}
-
-func applyFixes(result doctorResult) {
-	// Collect all fixable issues
-	var fixableIssues []doctorCheck
-	for _, check := range result.Checks {
-		if (check.Status == statusWarning || check.Status == statusError) && check.Fix != "" {
-			fixableIssues = append(fixableIssues, check)
-		}
-	}
-
-	if len(fixableIssues) == 0 {
-		fmt.Println("\nNo fixable issues found.")
-		return
-	}
-
-	// Show what will be fixed
-	fmt.Println("\nFixable issues:")
-	for i, issue := range fixableIssues {
-		fmt.Printf("  %d. %s: %s\n", i+1, issue.Name, issue.Message)
-	}
-
-	// Interactive mode - confirm each fix individually
-	if doctorInteractive {
-		applyFixesInteractive(result.Path, fixableIssues)
-		return
-	}
-
-	// Ask for confirmation (skip if --yes flag is set)
-	if !doctorYes {
-		fmt.Printf("\nThis will attempt to fix %d issue(s). Continue? (Y/n): ", len(fixableIssues))
-		reader := bufio.NewReader(os.Stdin)
-		response, err := reader.ReadString('\n')
-		if err != nil {
-			fmt.Fprintf(os.Stderr, "Error reading input: %v\n", err)
-			return
-		}
-
-		response = strings.TrimSpace(strings.ToLower(response))
-		if response != "" && response != "y" && response != "yes" {
-			fmt.Println("Fix canceled.")
-			return
-		}
-	}
-
-	// Apply fixes
-	fmt.Println("\nApplying fixes...")
-	applyFixList(result.Path, fixableIssues)
-}
-
-// applyFixesInteractive prompts for each fix individually
-func applyFixesInteractive(path string, issues []doctorCheck) {
-	reader := bufio.NewReader(os.Stdin)
-	applyAll := false
-	var approvedFixes []doctorCheck
-
-	fmt.Println("\nReview each fix:")
-	fmt.Println("  [y]es - apply this fix")
-	fmt.Println("  [n]o  - skip this fix")
-	fmt.Println("  [a]ll - apply all remaining fixes")
-	fmt.Println("  [q]uit - stop without applying more fixes")
-	fmt.Println()
-
-	for i, issue := range issues {
-		// Show issue details
-		fmt.Printf("(%d/%d) %s\n", i+1, len(issues), issue.Name)
-		if issue.Status == statusError {
-			fmt.Printf("  Status: %s\n", ui.RenderFail("ERROR"))
-		} else {
-			fmt.Printf("  Status: %s\n", ui.RenderWarn("WARNING"))
-		}
-		fmt.Printf("  Issue:  %s\n", issue.Message)
-		if issue.Detail != "" {
-			fmt.Printf("  Detail: %s\n", issue.Detail)
-		}
-		fmt.Printf("  Fix:    %s\n", issue.Fix)
-
-		// Check if we should apply all remaining
-		if applyAll {
-			fmt.Println("  → Auto-approved (apply all)")
-			approvedFixes = append(approvedFixes, issue)
-			continue
-		}
-
-		// Prompt for this fix
-		fmt.Print("\n  Apply this fix? [y/n/a/q]: ")
-		response, err := reader.ReadString('\n')
-		if err != nil {
-			fmt.Fprintf(os.Stderr, "Error reading input: %v\n", err)
-			return
-		}
-
-		response = strings.TrimSpace(strings.ToLower(response))
-		switch response {
-		case "y", "yes":
-			approvedFixes = append(approvedFixes, issue)
-			fmt.Println("  → Approved")
-		case "n", "no", "":
-			fmt.Println("  → Skipped")
-		case "a", "all":
-			applyAll = true
-			approvedFixes = append(approvedFixes, issue)
-			fmt.Println("  → Approved (applying all remaining)")
-		case "q", "quit":
-			fmt.Println("  → Quit")
-			if len(approvedFixes) > 0 {
-				fmt.Printf("\nApplying %d approved fix(es)...\n", len(approvedFixes))
-				applyFixList(path, approvedFixes)
-			} else {
-				fmt.Println("\nNo fixes applied.")
-			}
-			return
-		default:
-			// Treat unknown input as skip
-			fmt.Println("  → Skipped (unrecognized input)")
-		}
-		fmt.Println()
-	}
-
-	// Apply all approved fixes
-	if len(approvedFixes) > 0 {
-		fmt.Printf("\nApplying %d approved fix(es)...\n", len(approvedFixes))
-		applyFixList(path, approvedFixes)
-	} else {
-		fmt.Println("\nNo fixes approved.")
-	}
-}
-
-// applyFixList applies a list of fixes and reports results
-func applyFixList(path string, fixes []doctorCheck) {
-	// Apply fixes in a dependency-aware order.
-	// Rough dependency chain:
-	// permissions/daemon cleanup → config sanity → DB integrity/migrations → DB↔JSONL sync.
-	order := []string{
-		"Permissions",
-		"Daemon Health",
-		"Database Config",
-		"JSONL Config",
-		"Database Integrity",
-		"Database",
-		"Schema Compatibility",
-		"JSONL Integrity",
-		"DB-JSONL Sync",
-	}
-	priority := make(map[string]int, len(order))
-	for i, name := range order {
-		priority[name] = i
-	}
-	slices.SortStableFunc(fixes, func(a, b doctorCheck) int {
-		pa, oka := priority[a.Name]
-		if !oka {
-			pa = 1000
-		}
-		pb, okb := priority[b.Name]
-		if !okb {
-			pb = 1000
-		}
-		if pa < pb {
-			return -1
-		}
-		if pa > pb {
-			return 1
-		}
-		return 0
-	})
-
-	fixedCount := 0
-	errorCount := 0
-
-	for _, check := range fixes {
-		fmt.Printf("\nFixing %s...\n", check.Name)
-
-		var err error
-		switch check.Name {
-		case "Gitignore":
-			err = doctor.FixGitignore()
-		case "Git Hooks":
-			err = fix.GitHooks(path)
-		case "Daemon Health":
-			err = fix.Daemon(path)
-		case "DB-JSONL Sync":
-			err = fix.DBJSONLSync(path)
-		case "Permissions":
-			err = fix.Permissions(path)
-		case "Database":
-			err = fix.DatabaseVersion(path)
-		case "Database Integrity":
-			// Corruption detected - try recovery from JSONL
-			err = fix.DatabaseCorruptionRecovery(path)
-		case "Schema Compatibility":
-			err = fix.SchemaCompatibility(path)
-		case "Repo Fingerprint":
-			err = fix.RepoFingerprint(path)
-		case "Git Merge Driver":
-			err = fix.MergeDriver(path)
-		case "Sync Branch Config":
-			// No auto-fix: sync-branch should be added to config.yaml (version controlled)
-			fmt.Printf("  ⚠ Add 'sync-branch: beads-sync' to .beads/config.yaml\n")
-			continue
-		case "Database Config":
-			err = fix.DatabaseConfig(path)
-		case "JSONL Config":
-			err = fix.LegacyJSONLConfig(path)
-		case "JSONL Integrity":
-			err = fix.JSONLIntegrity(path)
-		case "Deletions Manifest":
-			err = fix.MigrateTombstones(path)
-		case "Untracked Files":
-			err = fix.UntrackedJSONL(path)
-		case "Sync Branch Health":
-			// Get sync branch from config
-			syncBranch := syncbranch.GetFromYAML()
-			if syncBranch == "" {
-				fmt.Printf("  ⚠ No sync branch configured in config.yaml\n")
-				continue
-			}
-			err = fix.SyncBranchHealth(path, syncBranch)
-		case "Merge Artifacts":
-			err = fix.MergeArtifacts(path)
-		case "Orphaned Dependencies":
-			err = fix.OrphanedDependencies(path)
-		case "Child-Parent Dependencies":
-			// Requires explicit opt-in flag (destructive, may remove intentional deps)
-			if !doctorFixChildParent {
-				fmt.Printf("  ⚠ Child→parent deps require explicit opt-in: bd doctor --fix --fix-child-parent\n")
-				continue
-			}
-			err = fix.ChildParentDependencies(path)
-		case "Duplicate Issues":
-			// No auto-fix: duplicates require user review
-			fmt.Printf("  ⚠ Run 'bd duplicates' to review and merge duplicates\n")
-			continue
-		case "Test Pollution":
-			// No auto-fix: test cleanup requires user review
-			fmt.Printf("  ⚠ Run 'bd doctor --check=pollution' to review and clean test issues\n")
-			continue
-		case "Git Conflicts":
-			// No auto-fix: git conflicts require manual resolution
-			fmt.Printf("  ⚠ Resolve conflicts manually: git checkout --ours or --theirs .beads/issues.jsonl\n")
-			continue
-		case "Stale Closed Issues":
-			// consolidate cleanup into doctor --fix
-			err = fix.StaleClosedIssues(path)
-		case "Expired Tombstones":
-			// consolidate cleanup into doctor --fix
-			err = fix.ExpiredTombstones(path)
-		case "Compaction Candidates":
-			// No auto-fix: compaction requires agent review
-			fmt.Printf("  ⚠ Run 'bd compact --analyze' to review candidates\n")
-			continue
-		case "Large Database":
-			// No auto-fix: pruning deletes data, must be user-controlled
-			fmt.Printf("  ⚠ Run 'bd cleanup --older-than 90' to prune old closed issues\n")
-			continue
-		default:
-			fmt.Printf("  ⚠ No automatic fix available for %s\n", check.Name)
-			fmt.Printf("  Manual fix: %s\n", check.Fix)
-			continue
-		}
-
-		if err != nil {
-			errorCount++
-			fmt.Printf("  %s Error: %v\n", ui.RenderFail("✗"), err)
-			fmt.Printf("  Manual fix: %s\n", check.Fix)
-		} else {
-			fixedCount++
-			fmt.Printf("  %s Fixed\n", ui.RenderPass("✓"))
-		}
-	}
-
-	// Summary
-	fmt.Printf("\nFix summary: %d fixed, %d errors\n", fixedCount, errorCount)
-	if errorCount > 0 {
-		fmt.Println("\nSome fixes failed. Please review the errors above and apply manual fixes as needed.")
-	}
-}
-
-// runCheckHealth runs lightweight health checks for git hooks.
-// Silent on success, prints a hint if issues detected.
-// Respects hints.doctor config setting.
-func runCheckHealth(path string) {
-	beadsDir := filepath.Join(path, ".beads")
-
-	// Check if .beads/ exists
-	if _, err := os.Stat(beadsDir); os.IsNotExist(err) {
-		// No .beads directory - nothing to check
-		return
-	}
-
-	// Get database path once (centralized path resolution)
-	dbPath := getCheckHealthDBPath(beadsDir)
-
-	// Check if database exists
-	if _, err := os.Stat(dbPath); os.IsNotExist(err) {
-		// No database - only check hooks
-		if issue := doctor.CheckHooksQuick(Version); issue != "" {
-			printCheckHealthHint([]string{issue})
-		}
-		return
-	}
-
-	// Open database once for all checks (single DB connection)
-	db, err := sql.Open("sqlite3", "file:"+dbPath+"?mode=ro")
-	if err != nil {
-		// Can't open DB - only check hooks
-		if issue := doctor.CheckHooksQuick(Version); issue != "" {
-			printCheckHealthHint([]string{issue})
-		}
-		return
-	}
-	defer db.Close()
-
-	// Check if hints.doctor is disabled in config
-	if hintsDisabledDB(db) {
-		return
-	}
-
-	// Run lightweight checks
-	var issues []string
-
-	// Check 1: Database version mismatch (CLI vs database bd_version)
-	if issue := checkVersionMismatchDB(db); issue != "" {
-		issues = append(issues, issue)
-	}
-
-	// Check 2: Sync branch not configured (now reads from config.yaml, not DB)
-	if issue := doctor.CheckSyncBranchQuick(); issue != "" {
-		issues = append(issues, issue)
-	}
-
-	// Check 3: Outdated git hooks
-	if issue := doctor.CheckHooksQuick(Version); issue != "" {
-		issues = append(issues, issue)
-	}
-
-	// Check 3: Sync-branch hook compatibility (issue #532)
-	if issue := doctor.CheckSyncBranchHookQuick(path); issue != "" {
-		issues = append(issues, issue)
-	}
-
-	// If any issues found, print hint
-	if len(issues) > 0 {
-		printCheckHealthHint(issues)
-	}
-	// Silent exit on success
-}
-
-// runDeepValidation runs full graph integrity validation
-func runDeepValidation(path string) {
-	// Show warning about potential slowness
-	fmt.Println("Running deep validation (may be slow on large databases)...")
-	fmt.Println()
-
-	result := doctor.RunDeepValidation(path)
-
-	if jsonOutput {
-		jsonBytes, err := doctor.DeepValidationResultJSON(result)
-		if err != nil {
-			fmt.Fprintf(os.Stderr, "Error: %v\n", err)
-			os.Exit(1)
-		}
-		fmt.Println(string(jsonBytes))
-	} else {
-		doctor.PrintDeepValidationResult(result)
-	}
-
-	if !result.OverallOK {
-		os.Exit(1)
-	}
-}
-
-// printCheckHealthHint prints the health check hint and exits with error.
-func printCheckHealthHint(issues []string) {
-	fmt.Fprintf(os.Stderr, "💡 bd doctor recommends a health check:\n")
-	for _, issue := range issues {
-		fmt.Fprintf(os.Stderr, "   • %s\n", issue)
-	}
-	fmt.Fprintf(os.Stderr, "   Run 'bd doctor' for details, or 'bd doctor --fix' to auto-repair\n")
-	fmt.Fprintf(os.Stderr, "   (Suppress with: bd config set %s false)\n", ConfigKeyHintsDoctor)
-	os.Exit(1)
-}
-
-// getCheckHealthDBPath returns the database path for check-health operations.
-// This centralizes the path resolution logic.
-func getCheckHealthDBPath(beadsDir string) string {
-	if cfg, err := configfile.Load(beadsDir); err == nil && cfg != nil && cfg.Database != "" {
-		return cfg.DatabasePath(beadsDir)
-	}
-	return filepath.Join(beadsDir, beads.CanonicalDatabaseName)
-}
-
-// hintsDisabledDB checks if hints.doctor is set to "false" using an existing DB connection.
-// Used by runCheckHealth to avoid multiple DB opens.
-func hintsDisabledDB(db *sql.DB) bool {
-	var value string
-	err := db.QueryRow("SELECT value FROM config WHERE key = ?", ConfigKeyHintsDoctor).Scan(&value)
-	if err != nil {
-		return false // Key not set, assume hints enabled
-	}
-	return strings.ToLower(value) == "false"
-}
-
-// checkVersionMismatchDB checks if CLI version differs from database bd_version.
-// Uses an existing DB connection.
-func checkVersionMismatchDB(db *sql.DB) string {
-	var dbVersion string
-	err := db.QueryRow("SELECT value FROM metadata WHERE key = 'bd_version'").Scan(&dbVersion)
-	if err != nil {
-		return "" // Can't read version, skip
-	}
-
-	if dbVersion != "" && dbVersion != Version {
-		return fmt.Sprintf("Version mismatch (CLI: %s, database: %s)", Version, dbVersion)
-	}
-
-	return ""
-}
-
 func runDiagnostics(path string) doctorResult {
 	result := doctorResult{
 		Path:       path,
@@ -1150,146 +688,3 @@ func printDiagnostics(result doctorResult) {
 	}
 }

-// 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")
-}