feat: Complete GH #353 follow-up phases (bd-9nw, bd-u3t, bd-e0o)

Implements all three follow-up phases for sandbox environment support:

**Phase 1 (bd-9nw): Documentation** ✅
- Comprehensive sandbox troubleshooting section in TROUBLESHOOTING.md
  - Detailed symptoms, root causes, and escape hatches
  - Step-by-step troubleshooting workflow
  - Comparison table for --sandbox, --force, and --allow-stale flags
- Global flags section added to CLI_REFERENCE.md
  - Documents --sandbox, --allow-stale, and --force flags
  - Usage examples and when to use each flag
- GitHub issue #353 comment with immediate workarounds

**Phase 2 (bd-u3t): Sandbox Auto-Detection** ✅
- Automatic sandbox detection using syscall.Kill permission checks
  - cmd/bd/sandbox_unix.go: Unix/Linux/macOS implementation
  - cmd/bd/sandbox_windows.go: Windows stub (conservative approach)
  - cmd/bd/sandbox_test.go: Comprehensive test coverage
- Auto-enables sandbox mode when detected
  - Shows: "ℹ️  Sandbox detected, using direct mode"
  - Respects explicit --sandbox or --no-daemon flags
- Updated documentation to reflect auto-detection (v0.21.1+)

**Phase 3 (bd-e0o): Enhanced Daemon Robustness** ✅
- Permission-aware process checks in cmd/bd/daemon_unix.go
  - Correctly handles EPERM (operation not permitted) from syscall.Kill
  - Treats EPERM as "process exists but not signable" = running
  - Prevents false negatives in sandboxed environments
- Metadata health check in cmd/bd/daemon_event_loop.go
  - Periodic verification that metadata is accessible
  - Helps detect external import operations (bd import --force)
  - Non-fatal logging for diagnostics
- Comprehensive test suite in cmd/bd/daemon_unix_test.go
  - Self-check, init process, nonexistent process, parent process tests

**Impact:**
- Codex users: No manual intervention needed, auto-detected
- Stuck states: Three escape hatches (--sandbox, --force, --allow-stale)
- Daemon robustness: Handles permission-restricted environments gracefully
- All three follow-up issues (bd-9nw, bd-u3t, bd-e0o) closed

**Files changed:**
- cmd/bd/main.go: Auto-detection logic in PersistentPreRun
- cmd/bd/sandbox_unix.go: Unix sandbox detection (new)
- cmd/bd/sandbox_windows.go: Windows sandbox detection stub (new)
- cmd/bd/sandbox_test.go: Sandbox detection tests (new)
- cmd/bd/daemon_unix.go: Permission-aware isProcessRunning()
- cmd/bd/daemon_unix_test.go: Process check tests (new)
- cmd/bd/daemon_event_loop.go: Metadata health check
- docs/TROUBLESHOOTING.md: Comprehensive sandbox section
- docs/CLI_REFERENCE.md: Global flags documentation

Closes bd-9nw, bd-u3t, bd-e0o
Related: GH #353

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

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

cmd/bd/main.go

@@ -200,6 +200,15 @@ var rootCmd = &cobra.Command{
 			return
 		}
 
+		// Auto-detect sandboxed environment (bd-u3t: Phase 2 for GH #353)
+		// Only auto-enable if user hasn't explicitly set --sandbox or --no-daemon
+		if !cmd.Flags().Changed("sandbox") && !cmd.Flags().Changed("no-daemon") {
+			if isSandboxed() {
+				sandboxMode = true
+				fmt.Fprintf(os.Stderr, "ℹ️  Sandbox detected, using direct mode\n")
+			}
+		}
+
 		// If sandbox mode is set, enable all sandbox flags
 		if sandboxMode {
 			noDaemon = true