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>

integrations/beads-mcp/README.md

@@ -288,7 +288,7 @@ Test daemon RPC with multiple repositories:
 ```bash
 # Start the daemon first
 cd /path/to/beads
-./bd daemon start
+./bd daemon --start
 
 # Run multi-repo test
 cd integrations/beads-mcp

integrations/beads-mcp/SETUP_DAEMON.md

@@ -137,7 +137,7 @@ bd daemon --start
 
 1. Check where daemon is running:
    ```bash
-   bd daemon status
+   bd daemon --status
    ```
 
 2. Use `set_context` tool in Claude to set workspace root: