Use a manual timeout implementation in Analysis to handle I/O gracefully

[rmosolgo]

Timeout::timeout may interrupt I/O operations leading to messed up connection handles. By implementing the timeout in Ruby instead, we can be sure that I/O operations will have terminated cleanly.

Downsides: a long-running I/O operation will not be killed halfway through. To mitigate this, you'll need timeouts on your client libraries themselves. Also, the timeout is only checked periodically so it's not 100% accurate (runtime may be a tiny bit longer than the timeout).

Also I removed on_fragment_definition. This is because the super(query.selected_operation) line in def initialize means that fragment definitions are never actually visited. I discovered this because I added a check_timeout to the old def on_fragment_definition and I couldn't get a test to fail for it 🤦

part of #5261