docs: fix bd daemon CLI syntax to use flag format (#568)

The bd daemon command only accepts flags with '--' prefix, not subcommands.
Fixed all documentation to use correct syntax:

- bd daemon start -> bd daemon --start
- bd daemon status -> bd daemon --status
- bd daemon stop -> bd daemon --stop
- bd daemon restart -> bd daemon --stop && bd daemon --start

Files updated:
- docs/PROTECTED_BRANCHES.md (13 occurrences)
- examples/team-workflow/README.md (4 occurrences)
- examples/protected-branch/README.md (3 occurrences)
- examples/multi-phase-development/README.md (1 occurrence)
- examples/multiple-personas/README.md (1 occurrence)
- integrations/beads-mcp/README.md (1 occurrence)
- integrations/beads-mcp/SETUP_DAEMON.md (1 occurrence)

Co-authored-by: cc-vps <crcatala+vps@gmail.com>

examples/protected-branch/README.md

@@ -52,7 +52,7 @@ bd update bd-XXXXX --status in_progress
 
 ```bash
 # Start daemon with auto-commit
-bd daemon start --auto-commit
+bd daemon --start --auto-commit
 
 # All issue changes are now automatically committed to beads-metadata branch
 ```
@@ -221,14 +221,14 @@ JSONL is append-only and line-based, so conflicts are rare. If they occur:
 The daemon creates it automatically on first commit. To create manually:
 ```bash
 bd config get sync.branch  # Verify it's set
-bd daemon restart          # Daemon will create worktree
+bd daemon --stop && bd daemon --start          # Daemon will create worktree
 ```
 
 **"Changes not syncing"**
 
 Make sure:
 - `bd config get sync.branch` returns the same value on all clones
-- Daemon is running: `bd daemon status`
+- Daemon is running: `bd daemon --status`
 - Both clones have fetched: `git fetch origin beads-metadata`
 
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