fix: Correct git merge driver placeholders from %L/%R to %A/%B

Git merge drivers only support three placeholders:
- %O (ancestor/base)
- %A (current version)
- %B (other branch's version)

The code was incorrectly using %L and %R, which don't exist in git,
causing them to be passed through literally and breaking JSONL merges.

Changes:
- Fixed merge driver config in init.go, merge.go, README.md, docs
- Added detection in bd doctor with clear error messages
- Added auto-fix in bd doctor --fix
- Added proactive warning in bd sync before git pull
- Added reactive error detection after merge failures
- Updated all tests to use correct placeholders

Now users get helpful guidance at every step:
1. bd doctor detects the issue
2. bd doctor --fix auto-corrects it
3. bd sync warns before pulling if misconfigured
4. Error messages suggest bd doctor --fix when merge fails

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

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

cmd/bd/doctor.go

@@ -8,6 +8,7 @@ import (
 	"io"
 	"net/http"
 	"os"
+	"os/exec"
 	"path/filepath"
 	"strings"
 	"time"
@@ -192,6 +193,8 @@ func applyFixes(result doctorResult) {
 			err = fix.DatabaseVersion(result.Path)
 		case "Schema Compatibility":
 			err = fix.SchemaCompatibility(result.Path)
+		case "Git Merge Driver":
+			err = fix.MergeDriver(result.Path)
 		default:
 			fmt.Printf("  ⚠ No automatic fix available for %s\n", check.Name)
 			fmt.Printf("  Manual fix: %s\n", check.Fix)
@@ -327,6 +330,11 @@ func runDiagnostics(path string) doctorResult {
 	result.Checks = append(result.Checks, gitignoreCheck)
 	// Don't fail overall check for gitignore, just warn
 
+	// Check 15: Git merge driver configuration
+	mergeDriverCheck := checkMergeDriver(path)
+	result.Checks = append(result.Checks, mergeDriverCheck)
+	// Don't fail overall check for merge driver, just warn
+
 	return result
 }
 
@@ -1513,6 +1521,64 @@ func checkSchemaCompatibility(path string) doctorCheck {
 	}
 }
 
+func checkMergeDriver(path string) doctorCheck {
+	// Check if we're in a git repository
+	gitDir := filepath.Join(path, ".git")
+	if _, err := os.Stat(gitDir); os.IsNotExist(err) {
+		return doctorCheck{
+			Name:    "Git Merge Driver",
+			Status:  statusOK,
+			Message: "N/A (not a git repository)",
+		}
+	}
+
+	// Get current merge driver configuration
+	cmd := exec.Command("git", "config", "merge.beads.driver")
+	cmd.Dir = path
+	output, err := cmd.Output()
+	if err != nil {
+		// Merge driver not configured
+		return doctorCheck{
+			Name:    "Git Merge Driver",
+			Status:  statusWarning,
+			Message: "Git merge driver not configured",
+			Fix:     "Run 'bd init' to configure the merge driver, or manually: git config merge.beads.driver \"bd merge %A %O %A %B\"",
+		}
+	}
+
+	currentConfig := strings.TrimSpace(string(output))
+	correctConfig := "bd merge %A %O %A %B"
+
+	// Check if using old incorrect placeholders
+	if strings.Contains(currentConfig, "%L") || strings.Contains(currentConfig, "%R") {
+		return doctorCheck{
+			Name:    "Git Merge Driver",
+			Status:  statusError,
+			Message: fmt.Sprintf("Incorrect merge driver config: %q (uses invalid %%L/%%R placeholders)", currentConfig),
+			Detail:  "Git only supports %O (base), %A (current), %B (other). Using %L/%R causes merge failures.",
+			Fix:     "Run 'bd doctor --fix' to update to correct config, or manually: git config merge.beads.driver \"bd merge %A %O %A %B\"",
+		}
+	}
+
+	// Check if config is correct
+	if currentConfig != correctConfig {
+		return doctorCheck{
+			Name:    "Git Merge Driver",
+			Status:  statusWarning,
+			Message: fmt.Sprintf("Non-standard merge driver config: %q", currentConfig),
+			Detail:  fmt.Sprintf("Expected: %q", correctConfig),
+			Fix:     fmt.Sprintf("Run 'bd doctor --fix' to update config, or manually: git config merge.beads.driver \"%s\"", correctConfig),
+		}
+	}
+
+	return doctorCheck{
+		Name:    "Git Merge Driver",
+		Status:  statusOK,
+		Message: "Correctly configured",
+		Detail:  currentConfig,
+	}
+}
+
 func init() {
 	rootCmd.AddCommand(doctorCmd)
 	doctorCmd.Flags().BoolVar(&perfMode, "perf", false, "Run performance diagnostics and generate CPU profile")