Coverage requires files to have same directory structure

[viveksjain]

Coverage was not working for our repository. I saw a hint in #1453 that the folder structure has to match the package names. When I made that match, I got coverage for those files. I have 2 followup questions:

1. I didn't see this documented anywhere and spent quite a while trying to get coverage working, it would have been very helpful to mention this in docs/coverage.md
2. Does this limitation come from rules_scala or jacoco, and is there a way to not require it? I tried --instrumentation_filter '.*' but that didn't help.

[FrankPortman]

Interestingly enough we just went down this rabbit hole at my company and similarly discovered that the source code tree has to match package names with trial and error. It would be awesome if this were not required (we are currently debating if it is worth it) but in lieu of that, clear documentation would be much appreciated.