`upgrade` does not properly exclude files from patching when RN is within a subdirectory

[bradjones1]

Environment

System:
    OS: Linux 5.17 Debian GNU/Linux 10 (buster) 10 (buster)
    CPU: (12) x64 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz
    Memory: 435.51 MB / 15.33 GB
    Shell: 5.0.3 - /bin/bash
  Binaries:
    Node: 16.13.1 - /tmp/yarn--1654921762795-0.3391503797865518/node
    Yarn: 1.22.15 - /tmp/yarn--1654921762795-0.3391503797865518/yarn
    npm: 8.1.2 - /usr/local/bin/npm
    Watchman: Not Found
  SDKs:
    Android SDK: Not Found
  IDEs:
    Android Studio: Not Found
  Languages:
    Java: Not Found
  npmPackages:
    @react-native-community/cli: Not Found
    react: 17.0.2 => 17.0.2 
    react-native: 0.68.1 => 0.68.1 
  npmGlobalPackages:
    *react-native*: Not Found

Description

When upgrading using react-native upgrade for a project which is in a subdirectory below the repository root, files which cannot be patched (e.g., because they have been edited from the prior version's defaults) are not properly excluded.

I believe this is a regression from https://github.com/react-native-community/cli/pull/272.

Reproducible Demo

Upgrade a project within a subdirectory of the project repo, with files which have changed from the prior version's defaults. Files which should be excluded will fail does not exist in index.