feat: start use tool permission confirmation struct (#2044)

crates/goose/src/agents/mod.rs

@@ -1,9 +1,7 @@
 mod agent;
-mod capabilities;
+pub mod capabilities;
 pub mod extension;
 mod factory;
-mod permission_judge;
-mod permission_store;
 mod reference;
 mod summarize;
 mod truncate;
@@ -13,5 +11,3 @@ pub use agent::{Agent, SessionConfig};
 pub use capabilities::Capabilities;
 pub use extension::ExtensionConfig;
 pub use factory::{register_agent, AgentFactory};
-pub use permission_judge::detect_read_only_tools;
-pub use permission_store::ToolPermissionStore;