WIP: Ticket40004: Use multi-phase approach to launch single-onion network.

In #40004 (closed), we found that turning off AssumeReachable made the single-onion tests fail. This appears to be due to a timing issue, where the onion services build their descriptors before the network is done bootstrapping.

Fortunately, chutney already has a multi-phase approach for network configuration: nodes can be configured or launched one phase at a time. So all we needed to do was to put the authorities and relays into "phase 1" and the other nodes in "phase 2".

But there was more work to do here: The wait_for_bootstrap command didn't know about phases, and the test-network.sh scripts didn't know about them either. I had to tweak the scripts a bit to make those work too.

With this change, "make test-network" passes again for me.