Better handle subdirectoried project on `upgrade`

[bradjones1]

Summary:

Fixes https://github.com/react-native-community/cli/issues/1622

Test Plan:

Upgrade a RN project which is in a subdirectory of a repository, and has non-patchable files (e.g., they changed from the prior version's distributed copy.) Upgrade will fail to patch any files. This also adds an environment variable to further exclude files that might have been changed and will be in a dirty state (e.g., after expo upgrade.)

[bradjones1]

I apologize I didn't touch the test coverage here... this came about as part of an upgrade on a project I'm cranking on and my Jest is even worse than my TypeScript - which is to say, it's non-existent. Hopefully this is clear enough, though.

[github-actions[bot]]

There hasn't been any activity on this pull request in the past 3 months, so it has been marked as stale and it will be closed automatically if no further activity occurs in the next 7 days.