[Feature]: Finer granular control/integration of file guard and tool guard

Currently, file guard is a blacklist, all directory path set in file guard will not be accessed at all, but for some directory path it would handy to be read-only for agent.
Also, all other path not set in file guard follow same tool guard rules, but we may want to have a whitelist as project directories to have different sets of tool guard rules. For example, the agent would not need permission for deleting cache or temporary files every time.