chore: rename bash tool to shell for cross-shell compatibility

[dl-alexandre]

The Go TUI was renamed from 'bash' to 'shell' in commit a4beb60e to better reflect that the tool works with multiple shells (zsh, fish, nu, cmd.exe, etc.), not just bash. This commit applies the same rename to the TypeScript/Node.js server side to maintain consistency.

Changes:

• Rename tool definition from 'bash' to 'shell'
• Update all permission type references throughout agent and config schemas
• Update tool type checks in CLI, web components, and TUI registry
• Remove TODO comment that prompted this change

This aligns the server implementation with the already-renamed Go TUI client.