refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

Analysis found these commands are dead code:
- gt never calls `bd pin` - uses `bd update --status=pinned` instead
- Beads.Pin() wrapper exists but is never called
- bd hook functionality duplicated by gt mol status
- Code comment says "pinned field is cosmetic for bd hook visibility"

Removed:
- cmd/bd/pin.go
- cmd/bd/unpin.go
- cmd/bd/hook.go

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

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

cmd/bd/doctor_repair_test.go

@@ -0,0 +1,151 @@
+package main
+
+import (
+	"encoding/json"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"runtime"
+	"strings"
+	"testing"
+)
+
+func buildBDForTest(t *testing.T) string {
+	t.Helper()
+	exeName := "bd"
+	if runtime.GOOS == "windows" {
+		exeName = "bd.exe"
+	}
+
+	binDir := t.TempDir()
+	exe := filepath.Join(binDir, exeName)
+	cmd := exec.Command("go", "build", "-o", exe, ".")
+	out, err := cmd.CombinedOutput()
+	if err != nil {
+		t.Fatalf("go build failed: %v\n%s", err, string(out))
+	}
+	return exe
+}
+
+func mkTmpDirInTmp(t *testing.T, prefix string) string {
+	t.Helper()
+	dir, err := os.MkdirTemp("/tmp", prefix)
+	if err != nil {
+		// Fallback for platforms without /tmp (e.g. Windows).
+		dir, err = os.MkdirTemp("", prefix)
+		if err != nil {
+			t.Fatalf("failed to create temp dir: %v", err)
+		}
+	}
+	t.Cleanup(func() { _ = os.RemoveAll(dir) })
+	return dir
+}
+
+func runBDSideDB(t *testing.T, exe, dir, dbPath string, args ...string) (string, error) {
+	t.Helper()
+	fullArgs := []string{"--db", dbPath}
+	if len(args) > 0 && args[0] != "init" {
+		fullArgs = append(fullArgs, "--no-daemon")
+	}
+	fullArgs = append(fullArgs, args...)
+
+	cmd := exec.Command(exe, fullArgs...)
+	cmd.Dir = dir
+	cmd.Env = append(os.Environ(),
+		"BEADS_NO_DAEMON=1",
+		"BEADS_DIR="+filepath.Join(dir, ".beads"),
+	)
+	out, err := cmd.CombinedOutput()
+	return string(out), err
+}
+
+func TestDoctorRepair_CorruptDatabase_RebuildFromJSONL(t *testing.T) {
+	if testing.Short() {
+		t.Skip("skipping slow repair test in short mode")
+	}
+
+	bdExe := buildBDForTest(t)
+	ws := mkTmpDirInTmp(t, "bd-doctor-repair-*")
+	dbPath := filepath.Join(ws, ".beads", "beads.db")
+	jsonlPath := filepath.Join(ws, ".beads", "issues.jsonl")
+
+	if _, err := runBDSideDB(t, bdExe, ws, dbPath, "init", "--prefix", "chaos", "--quiet"); err != nil {
+		t.Fatalf("bd init failed: %v", err)
+	}
+	if _, err := runBDSideDB(t, bdExe, ws, dbPath, "create", "Chaos issue", "-p", "1"); err != nil {
+		t.Fatalf("bd create failed: %v", err)
+	}
+	if _, err := runBDSideDB(t, bdExe, ws, dbPath, "export", "-o", jsonlPath, "--force"); err != nil {
+		t.Fatalf("bd export failed: %v", err)
+	}
+
+	// Corrupt the SQLite file (truncate) and verify doctor reports an integrity error.
+	if err := os.Truncate(dbPath, 128); err != nil {
+		t.Fatalf("truncate db: %v", err)
+	}
+
+	out, err := runBDSideDB(t, bdExe, ws, dbPath, "doctor", "--json")
+	if err == nil {
+		t.Fatalf("expected bd doctor to fail on corrupt db")
+	}
+	jsonStart := strings.Index(out, "{")
+	if jsonStart < 0 {
+		t.Fatalf("doctor output missing JSON: %s", out)
+	}
+	var before doctorResult
+	if err := json.Unmarshal([]byte(out[jsonStart:]), &before); err != nil {
+		t.Fatalf("unmarshal doctor json: %v\n%s", err, out)
+	}
+	var foundIntegrity bool
+	for _, c := range before.Checks {
+		if c.Name == "Database Integrity" {
+			foundIntegrity = true
+			if c.Status != statusError {
+				t.Fatalf("Database Integrity status=%q want %q", c.Status, statusError)
+			}
+		}
+	}
+	if !foundIntegrity {
+		t.Fatalf("Database Integrity check not found")
+	}
+
+	// Attempt auto-repair.
+	out, err = runBDSideDB(t, bdExe, ws, dbPath, "doctor", "--fix", "--yes")
+	if err != nil {
+		t.Fatalf("bd doctor --fix failed: %v\n%s", err, out)
+	}
+
+	// Doctor should now pass.
+	out, err = runBDSideDB(t, bdExe, ws, dbPath, "doctor", "--json")
+	if err != nil {
+		t.Fatalf("bd doctor after fix failed: %v\n%s", err, out)
+	}
+	jsonStart = strings.Index(out, "{")
+	if jsonStart < 0 {
+		t.Fatalf("doctor output missing JSON: %s", out)
+	}
+	var after doctorResult
+	if err := json.Unmarshal([]byte(out[jsonStart:]), &after); err != nil {
+		t.Fatalf("unmarshal doctor json: %v\n%s", err, out)
+	}
+	if !after.OverallOK {
+		t.Fatalf("expected overall_ok=true after repair")
+	}
+
+	// Data should still be present.
+	out, err = runBDSideDB(t, bdExe, ws, dbPath, "list", "--json")
+	if err != nil {
+		t.Fatalf("bd list failed after repair: %v\n%s", err, out)
+	}
+	jsonStart = strings.Index(out, "[")
+	if jsonStart < 0 {
+		t.Fatalf("list output missing JSON array: %s", out)
+	}
+	var issues []map[string]any
+	if err := json.Unmarshal([]byte(out[jsonStart:]), &issues); err != nil {
+		t.Fatalf("unmarshal list json: %v\n%s", err, out)
+	}
+	if len(issues) != 1 {
+		t.Fatalf("expected 1 issue after repair, got %d", len(issues))
+	}
+}