feat(doctor): add fresh clone detection check (bd-4ew)

Add CheckFreshClone function that detects when JSONL contains issues
but no database exists. Recommends 'bd init --prefix <detected-prefix>'
to hydrate the database. This check appears early in doctor output
to guide users on fresh clones.

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

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

cmd/bd/doctor/legacy.go

@@ -1,11 +1,14 @@
 package doctor
 
 import (
+	"bufio"
+	"encoding/json"
 	"fmt"
 	"os"
 	"path/filepath"
 	"strings"
 
+	"github.com/steveyegge/beads/internal/beads"
 	"github.com/steveyegge/beads/internal/configfile"
 )
 
@@ -330,3 +333,132 @@ func CheckDatabaseConfig(repoPath string) DoctorCheck {
 			"  3. Or rename the files to match the configuration",
 	}
 }
+
+// CheckFreshClone detects if this is a fresh clone that needs 'bd init'.
+// A fresh clone has JSONL with issues but no database file.
+// bd-4ew: Recommend 'bd init --prefix <detected-prefix>' for fresh clones.
+func CheckFreshClone(repoPath string) DoctorCheck {
+	beadsDir := filepath.Join(repoPath, ".beads")
+
+	// Check if .beads/ exists
+	if _, err := os.Stat(beadsDir); os.IsNotExist(err) {
+		return DoctorCheck{
+			Name:    "Fresh Clone",
+			Status:  "ok",
+			Message: "N/A (no .beads directory)",
+		}
+	}
+
+	// Find the JSONL file
+	var jsonlPath string
+	var jsonlName string
+	for _, name := range []string{"issues.jsonl", "beads.jsonl"} {
+		testPath := filepath.Join(beadsDir, name)
+		if _, err := os.Stat(testPath); err == nil {
+			jsonlPath = testPath
+			jsonlName = name
+			break
+		}
+	}
+
+	// No JSONL file - not a fresh clone situation
+	if jsonlPath == "" {
+		return DoctorCheck{
+			Name:    "Fresh Clone",
+			Status:  "ok",
+			Message: "N/A (no JSONL file)",
+		}
+	}
+
+	// Check if database exists
+	var dbPath string
+	if cfg, err := configfile.Load(beadsDir); err == nil && cfg != nil && cfg.Database != "" {
+		dbPath = cfg.DatabasePath(beadsDir)
+	} else {
+		// Fall back to canonical database name
+		dbPath = filepath.Join(beadsDir, beads.CanonicalDatabaseName)
+	}
+
+	// If database exists, not a fresh clone
+	if _, err := os.Stat(dbPath); err == nil {
+		return DoctorCheck{
+			Name:    "Fresh Clone",
+			Status:  "ok",
+			Message: "Database exists",
+		}
+	}
+
+	// Check if JSONL has any issues (empty JSONL = not really a fresh clone)
+	issueCount, prefix := countJSONLIssuesAndPrefix(jsonlPath)
+	if issueCount == 0 {
+		return DoctorCheck{
+			Name:    "Fresh Clone",
+			Status:  "ok",
+			Message: fmt.Sprintf("JSONL exists but is empty (%s)", jsonlName),
+		}
+	}
+
+	// This is a fresh clone! JSONL has issues but no database.
+	fixCmd := "bd init"
+	if prefix != "" {
+		fixCmd = fmt.Sprintf("bd init --prefix %s", prefix)
+	}
+
+	return DoctorCheck{
+		Name:    "Fresh Clone",
+		Status:  "warning",
+		Message: fmt.Sprintf("Fresh clone detected (%d issues in %s, no database)", issueCount, jsonlName),
+		Detail:  "This appears to be a freshly cloned repository.\n" +
+			"  The JSONL file contains issues but no local database exists.\n" +
+			"  Run 'bd init' to create the database and import existing issues.",
+		Fix: fmt.Sprintf("Run '%s' to initialize the database and import issues", fixCmd),
+	}
+}
+
+// countJSONLIssuesAndPrefix counts issues in a JSONL file and detects the most common prefix.
+func countJSONLIssuesAndPrefix(jsonlPath string) (int, string) {
+	file, err := os.Open(jsonlPath) //nolint:gosec
+	if err != nil {
+		return 0, ""
+	}
+	defer file.Close()
+
+	count := 0
+	prefixCounts := make(map[string]int)
+
+	scanner := bufio.NewScanner(file)
+	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 != "" {
+			count++
+			// Extract prefix (everything before the last dash)
+			if lastDash := strings.LastIndex(issue.ID, "-"); lastDash > 0 {
+				prefix := issue.ID[:lastDash]
+				prefixCounts[prefix]++
+			}
+		}
+	}
+
+	// Find most common prefix
+	var mostCommonPrefix string
+	maxCount := 0
+	for prefix, cnt := range prefixCounts {
+		if cnt > maxCount {
+			maxCount = cnt
+			mostCommonPrefix = prefix
+		}
+	}
+
+	return count, mostCommonPrefix
+}