doctor: add git hygiene checks and DB integrity auto-fix

Co-authored-by: factory-droid[bot] <138933559+factory-droid[bot]@users.noreply.github.com>

cmd/bd/doctor/fix/database_integrity.go

@@ -0,0 +1,134 @@
+package fix
+
+import (
+	"bufio"
+	"encoding/json"
+	"fmt"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"time"
+
+	"github.com/steveyegge/beads/internal/beads"
+	"github.com/steveyegge/beads/internal/configfile"
+	"github.com/steveyegge/beads/internal/utils"
+)
+
+// DatabaseIntegrity attempts to recover from database corruption by:
+//  1. Backing up the corrupt database (and WAL/SHM if present)
+//  2. Re-initializing the database from the git-tracked JSONL export
+//
+// This is intentionally conservative: it will not delete JSONL, and it preserves the
+// original DB as a backup for forensic recovery.
+func DatabaseIntegrity(path string) error {
+	if err := validateBeadsWorkspace(path); err != nil {
+		return err
+	}
+
+	absPath, err := filepath.Abs(path)
+	if err != nil {
+		return fmt.Errorf("failed to resolve path: %w", err)
+	}
+
+	beadsDir := filepath.Join(absPath, ".beads")
+
+	// Resolve database path (respects metadata.json database override).
+	var dbPath string
+	if cfg, err := configfile.Load(beadsDir); err == nil && cfg != nil && cfg.Database != "" {
+		dbPath = cfg.DatabasePath(beadsDir)
+	} else {
+		dbPath = filepath.Join(beadsDir, beads.CanonicalDatabaseName)
+	}
+
+	// Find JSONL source of truth.
+	jsonlPath := ""
+	if cfg, err := configfile.Load(beadsDir); err == nil && cfg != nil {
+		candidate := cfg.JSONLPath(beadsDir)
+		if _, err := os.Stat(candidate); err == nil {
+			jsonlPath = candidate
+		}
+	}
+	if jsonlPath == "" {
+		for _, name := range []string{"issues.jsonl", "beads.jsonl"} {
+			candidate := filepath.Join(beadsDir, name)
+			if _, err := os.Stat(candidate); err == nil {
+				jsonlPath = candidate
+				break
+			}
+		}
+	}
+	if jsonlPath == "" {
+		return fmt.Errorf("cannot auto-recover: no JSONL export found in %s", beadsDir)
+	}
+
+	// Back up corrupt DB and its sidecar files.
+	ts := time.Now().UTC().Format("20060102T150405Z")
+	backupDB := dbPath + "." + ts + ".corrupt.backup.db"
+	if err := os.Rename(dbPath, backupDB); err != nil {
+		return fmt.Errorf("failed to back up database: %w", err)
+	}
+	for _, suffix := range []string{"-wal", "-shm", "-journal"} {
+		sidecar := dbPath + suffix
+		if _, err := os.Stat(sidecar); err == nil {
+			_ = os.Rename(sidecar, backupDB+suffix) // best effort
+		}
+	}
+
+	// Rebuild via bd init, pointing at the same db path.
+	bdBinary, err := getBdBinary()
+	if err != nil {
+		return err
+	}
+
+	args := []string{"--db", dbPath, "init", "--quiet", "--force", "--skip-hooks", "--skip-merge-driver"}
+	if prefix := detectPrefixFromJSONL(jsonlPath); prefix != "" {
+		args = append(args, "--prefix", prefix)
+	}
+
+	cmd := exec.Command(bdBinary, args...) // #nosec G204 -- bdBinary is a validated executable path
+	cmd.Dir = absPath
+	cmd.Stdout = os.Stdout
+	cmd.Stderr = os.Stderr
+	cmd.Env = os.Environ()
+
+	if err := cmd.Run(); err != nil {
+		// Best-effort rollback: if init didn't recreate the db, restore the backup.
+		if _, statErr := os.Stat(dbPath); os.IsNotExist(statErr) {
+			_ = os.Rename(backupDB, dbPath)
+			for _, suffix := range []string{"-wal", "-shm", "-journal"} {
+				_ = os.Rename(backupDB+suffix, dbPath+suffix)
+			}
+		}
+		return fmt.Errorf("failed to rebuild database from JSONL: %w (backup: %s)", err, backupDB)
+	}
+
+	return nil
+}
+
+func detectPrefixFromJSONL(jsonlPath string) string {
+	f, err := os.Open(jsonlPath) // #nosec G304 -- jsonlPath is within the workspace
+	if err != nil {
+		return ""
+	}
+	defer f.Close()
+
+	scanner := bufio.NewScanner(f)
+	for scanner.Scan() {
+		line := scanner.Bytes()
+		if len(line) == 0 {
+			continue
+		}
+		var issue struct {
+			ID string `json:"id"`
+		}
+		if err := json.Unmarshal(line, &issue); err != nil {
+			continue
+		}
+		if issue.ID == "" {
+			continue
+		}
+		return utils.ExtractIssuePrefix(issue.ID)
+	}
+
+	return ""
+}