Cleanup skill logic files and update deployment scripts

Fix AI loop stalling and large file sync issues

fix(agent): use Optional type hint for Python 3.8 compatibility ...

- Fixes 'TypeError: unsupported operand type(s) for |' on Synology NAS.\n- Bumps version to 1.0.11 to trigger sync.

fix(agent): correct path to bootstrap_installer in updater ...

- Updated the relative path to 3 levels up to correctly find the bootstrapper in the agent-node root.\n- Bumping to 1.0.6.

refactor: organize agent-node client code structure by moving core packages to src/ ...

- Moved agent_node, protos, and shared_core inside src/

- Updated Dockerfile, deployment scripts, compile_protos.sh, installers

- Updated bundle generation in ai-hub to reflect cleaner structure and better README