Fixes plugins overwriting files outside of .devbox

[t-monaghan]

Summary

This PR is to address #1909

The issue was that the check for files in the .devbox/ directory was including files inside devbox.d/jetpack-io.devbox-plugins.{PLUGIN}/. This resulted in plugin configuration being overwritten where it shouldn't have been.

This solution is rudimentary, I just wanted to highlight what I think is the cause.

How was it tested?

On my machine, I replicated the issue and ensured that.

• Files inside .devbox/ are still being overwritten as expected
• Files outside of .devbox/ are no longer being overwritten
• devbox run test passes locally for this devbox build