codebase-documentation -- update core prompt

[DuHerb]

• Revert the maintenance prompts back to the templated custom prompts that are injected into the repo. Having the maintenance prompts as part of the plug-in package creates a dependency as well as prevents customization after initialization

• When asking clarification questions, the user should be able to define how the domains are scoped. I.e. right now it's Based on directory structure, but a user might want to define it domains as layers like data access, TAO, authentication. et cetera. Or there might be additional ways to break it up. For instance, the Mackers API had different services as domains controllers, et cetera. So a domain could have been a system or a common pattern. The user might also be able to pass in custom domains That the prop should be smart enough to investigate and create a map for.

• Need to refine the complexity. Like we want to make this not a burden to maintain, but a lightweight discovery tool for patterns, code styles, Do not can't all be located quickly without having to infer from ad hoc explorations.