Reduce flakiness of CI tests

[mattyg]

Reduce flakiness of ci tests by:

• ~Using cachix key with write permission to reduce nix environment setup time~ keep flakes.lock up to date
• Refactor tests to avoid using sleep() calls (waiting on https://github.com/holochain/tryorama/issues/167)

[jost-s]

Tests have been running stably on recent branches after increasing the zome call timeout.