Cmd flags can be provided through config file

[manusa]

Description

As a user/mcp admin, I want to be able to provide all configurations through a toml file, to be able to share configurations and minimize the entry-point arguments.

With the introduction of the TOML configuration file support #131, command flags for configuration can become cumbersome and redundant.

My initial proposal would be to keep the current configuration flags as a way to override configurations provided from the configuration file (flags have precedence over config file).

This would allow for one-off overrides for specific MCP executions.

New configurations should be managed through the config files with flags provided only for those that would make sense for a one-off execution.

[ardaguclu]

I've started implementing this. Probably I'll use viper to wire flags to configuration.