refactor(kernel): fix None leak and migrate core utilities to /core

[AkshajSinghal]

• Fix TruKernel _execute_entry to suppress printing of None return values.
• Move database.py, model.py, and settings.py into trushell/core/ for better encapsulation.
• Update all internal imports and test references to point to new trushell.core modules.
• Begin migration of legacy command logic (pyfunny) into commands/joke.py.
• Remove obsolete root-level utility files to reduce package clutter.

This refactor stabilizes the kernel's output handling and establishes the final internal directory structure before consolidating remaining legacy commands.

[AkshajSinghal]

Alright, this PR lands the core TruKernel engine. The manifest dispatch is working, OS fallback is live, and the None leak is fixed. I’ve also moved database, models, and settings into /core to clean up the root.

Heads up, I’m heading out. The migration isn’t 100% done.
These files are still sitting in the root but are effectively orphaned:

• todocli.py (needs to merge into commands/tasks.py)
• chronoterm/ (needs to merge into commands/chronoterm.py)
• project.py (delete it, cli.py handles the REPL now)

If anyone wants to grab this branch and finish the cleanup, be my guest. Just make sure pytest -q passes before you push.
Don’t break the build. Cheers!

[AkshajSinghal]

Implemented in #21