Remove and consolidate osquery instance options

[RebeccaMahany]

Relates to #1827 -- getting some tidying out of the way before making more substantial changes.

Relates to #1936.

This PR updates our osquery instance options:

1. Remove unused options
2. Remove options that are redundant with knapsack flags, opting to pull these values from the knapsack instead

While I was validating that the root directory will always be set by the time that we make it to the osquery runner, I noticed that in runLauncher if the root directory wasn't set in the launcher options and we fell back to making a temp directory, we wouldn't save that temp directory in the knapsack flags. I updated to save it in the launcher options, so that it would later be available via the knapsack. I imagine we don't run into this issue much/at all, but wanted to address it just in case.

[James-Pickett]

LGTM! Always love negative lines of code. Do any of these removals make options in launcher options obsolete?

[directionless]

I didn't test this, but I imagine it's fine.

However I think we should hold slightly on merging -- I think we're going to want to be in a place to cut a release for Zack's flare stuff and maybe the systray tweaks.

[RebeccaMahany]

@directionless good point -- converted to draft and will hold off on merging.

@James-Pickett checked and yes! Deprecated a handful of flags. 🎉