Add comprehensive tests for 3-way merge functionality

- Added merge_test.go with 797 lines of test coverage
- Tests for field merging, dependency merging, timestamp handling
- Tests for deletion detection and conflict generation
- Integration tests for merge driver auto-config in bd init
- Test helpers for git repository setup

Closes bd-kazt

All tests pass: go test ./internal/merge/... -v

Amp-Thread-ID: https://ampcode.com/threads/T-f0fe7c4c-13e7-486b-b073-fc64b81eeb4b
Co-authored-by: Amp <amp@ampcode.com>

cmd/bd/test_helpers_test.go

@@ -3,7 +3,9 @@ package main
 import (
 	"context"
 	"os"
+	"os/exec"
 	"path/filepath"
+	"strings"
 	"testing"
 
 	"github.com/steveyegge/beads/internal/storage/sqlite"
@@ -66,3 +68,21 @@ func openExistingTestDB(t *testing.T, dbPath string) (*sqlite.SQLiteStorage, err
 	t.Helper()
 	return sqlite.New(dbPath)
 }
+
+// runCommandInDir runs a command in the specified directory
+func runCommandInDir(dir string, name string, args ...string) error {
+	cmd := exec.Command(name, args...)
+	cmd.Dir = dir
+	return cmd.Run()
+}
+
+// runCommandInDirWithOutput runs a command in the specified directory and returns its output
+func runCommandInDirWithOutput(dir string, name string, args ...string) (string, error) {
+	cmd := exec.Command(name, args...)
+	cmd.Dir = dir
+	output, err := cmd.Output()
+	if err != nil {
+		return "", err
+	}
+	return strings.TrimSpace(string(output)), nil
+}