Function cmd_update 

pub fn cmd_update(
    beans_dir: &Path,
    id: &str,
    title: Option<String>,
    description: Option<String>,
    acceptance: Option<String>,
    notes: Option<String>,
    design: Option<String>,
    status: Option<String>,
    priority: Option<u8>,
    assignee: Option<String>,
    add_label: Option<String>,
    remove_label: Option<String>,
) -> Result<()>

Update a bean’s fields based on provided flags.

• title, description, acceptance, design, priority, assignee, status: replace
• notes: append with timestamp separator
• labels: add/remove operations
• updates updated_at and rebuilds index