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>

docs/CLI_REFERENCE.md

@@ -203,6 +203,83 @@ bd list --priority-min 2 --json                         # P2 and below
 bd list --status open --priority 1 --label-any urgent,critical --no-assignee --json
 ```
 
+## Global Flags
+
+Global flags work with any bd command and must appear **before** the subcommand.
+
+### Sandbox Mode
+
+**Auto-detection (v0.21.1+):** bd automatically detects sandboxed environments and enables sandbox mode.
+
+When detected, you'll see: `ℹ️  Sandbox detected, using direct mode`
+
+**Manual override:**
+
+```bash
+# Explicitly enable sandbox mode
+bd --sandbox <command>
+
+# Equivalent to combining these flags:
+bd --no-daemon --no-auto-flush --no-auto-import <command>
+```
+
+**What it does:**
+- Disables daemon (uses direct SQLite mode)
+- Disables auto-export to JSONL
+- Disables auto-import from JSONL
+
+**When to use:** Sandboxed environments where daemon can't be controlled (permission restrictions), or when auto-detection doesn't trigger.
+
+### Staleness Control
+
+```bash
+# Skip staleness check (emergency escape hatch)
+bd --allow-stale <command>
+
+# Example: access database even if out of sync with JSONL
+bd --allow-stale ready --json
+bd --allow-stale list --status open --json
+```
+
+**Shows:** `⚠️  Staleness check skipped (--allow-stale), data may be out of sync`
+
+**⚠️ Caution:** May show stale or incomplete data. Use only when stuck and other options fail.
+
+### Force Import
+
+```bash
+# Force metadata update even when DB appears synced
+bd import --force -i .beads/beads.jsonl
+```
+
+**When to use:** `bd import` reports "0 created, 0 updated" but staleness errors persist.
+
+**Shows:** `Metadata updated (database already in sync with JSONL)`
+
+### Other Global Flags
+
+```bash
+# JSON output for programmatic use
+bd --json <command>
+
+# Force direct mode (bypass daemon)
+bd --no-daemon <command>
+
+# Disable auto-sync
+bd --no-auto-flush <command>    # Disable auto-export to JSONL
+bd --no-auto-import <command>   # Disable auto-import from JSONL
+
+# Custom database path
+bd --db /path/to/.beads/beads.db <command>
+
+# Custom actor for audit trail
+bd --actor alice <command>
+```
+
+**See also:**
+- [TROUBLESHOOTING.md - Sandboxed environments](TROUBLESHOOTING.md#sandboxed-environments-codex-claude-code-etc) for detailed sandbox troubleshooting
+- [DAEMON.md](DAEMON.md) for daemon mode details
+
 ## Advanced Operations
 
 ### Cleanup