Remove remaining global config

[neubig]

What is the problem that this fixes or functionality that this introduces? Does it fix any open issues?

This removes the remaining global configuration. Finally done refactoring!

[WIP] because this still needs to be tested, please do not spend lots of time reviewing yet.

Give a summary of what the PR does, explaining any non-trivial design decisions

There are a few non-trivial things:

1. The file storage needs to be passed around a bit
2. The "parse arguments" function was setting the workspace_base variable, I removed this because it seems like a bit of an anti-pattern, but we probably need to make sure this doesn't break things.
3. I decided to pass in AppConfig to Runtime. I want to avoid using AppConfig as much as possible, as it requires/provides too much information, and obscures which information is actually used by the class. However, runtimes use lots of information and different runtimes use different types of information at the moment, so this seemed necessary to avoid further extensive refactoring.

Other references

Fixes #2758

[xingyaoww]

LGTM! Just a couple minor comments - i think it should be ready to merge once we fixed all the test cases

[neubig]

I have confirmed that tests pass and the app runs on my local machine, I think this is ready to merge!