Deprecate and remove --allowedTools, --excludeTools, --coreTools in favor of user defined policy

[allenhutchison]

[aidansommers]

When deprecating things such as --excludeTools, it would be helpful to know how excluding tools specific to extensions will be handled. Additionally, it would be helpful for the future of "--excludeTools" (however this is defined in the policy engine) to be aware that disabling and excluding can serve different purposes and imply different things. Disabling a tool from an extension / MCP server may still load the tool into context for the model (but may not allow the model to actually execute the tool), but excluding it could remove it from context entirely. As you can imagine, any context provided by a tool's inclusion may be important (or there may be desire to ignore it entirely). Any clarity on the future of this would be great!