configuration/installer scripts - handle dependencies better so as not to overwrite/lose user settings

[mmguero]

The following code in the installer script:

• dependencies.py
• dependency_manager.py
• malcolm_config.py

handles "dependencies," which are essentially "If setting A changes, that may result in a change to setting B" sorts of things.

For the most part this works very well, but there are some issues where a user's settings might be changed incorrectly: I think this happens during initial loading/setting up of the configuration item tree, even though it works correctly when being "user-driven."

I'm wondering if we need to change it so that during a load (loading from an exported file, loading from existing .env files) we "pause" the dependency resolving (making changes to "downstream" settings) until that initial loading is complete.

For example:

• On Hedgehog Linux, the default is that arkime-live is set as the default PCAP capture method. However, even if a user disables it (so that no PCAP capture method is enabled, which is totally valid), returning to the configuration will have it enabled again.
• Sometimes I notice that enabling/disabling zeek OT protocol scanners gets re-set when I come back into configuration.

There are others. This needs to be looked at.