feat: add thinking option support and autonomous run handling

packages/cli/src/commands/agent/index.ts

@@ -27,6 +27,7 @@ export function createAgentCommand(): Command {
     .option('-a, --all', 'Include archived agents')
     .option('-g, --global', 'Legacy no-op (kept for compatibility)')
     .option('--label <key=value>', 'Filter by label (can be used multiple times)', collectMultiple, [])
+    .option('--thinking <id>', 'Filter by thinking option ID')
     .option('--json', 'Output in JSON format')
     .option('--host <host>', 'Daemon host:port (default: localhost:6767)')
     .action(withOutput(runLsCommand))
@@ -39,6 +40,7 @@ export function createAgentCommand(): Command {
     .option('--name <name>', 'Assign a name/title to the agent')
     .option('--provider <provider>', 'Agent provider: claude | codex | opencode', 'claude')
     .option('--model <model>', 'Model to use (e.g., claude-sonnet-4-20250514, claude-3-5-haiku-20241022)')
+    .option('--thinking <id>', 'Thinking option ID to use for this run')
     .option('--mode <mode>', 'Provider-specific mode (e.g., plan, default, bypass)')
     .option('--cwd <path>', 'Working directory (default: current)')
     .option('--label <key=value>', 'Add label(s) to the agent (can be used multiple times)', collectMultiple, [])