Since a recent upgrade, I've found that sometimes I am getting a bunch of meta files created for files outside the Assets directory and that should not have meta files. These are mostly for csproj files. I just have to keep deleting them.
I can't 100% verify that it is Rider and not Unity causing this, but:
It's probably worth noting that our repository contains both standard Unity projects and a packages directory, and maybe this is confusing Rider and making it think the root is further up than normal.
@Kylotan What is your Rider version and Unity version? When this issue happens again, please list here paths of those meta files. A screenshot may help.
I tried to reproduce, but no, it doesn't happen.
Feel free to reopen the issue.
Sorry, should have remembered those details.
Can't share full paths due to client confidentiality but here are some examples of meta files that appeared in the directory that contains Assets.

Our team is experiencing the same issue. It happens on both Windows and macOS. Worst of all, the Rider plugin even causes the meta files to get created outside the folder of the repository.
Example folder structure:
Meta files get created for:
Solution explorer shows this:

Can you try reproducing it in a git repo where the Unity project is one folder down and there's a stylecop JSON file in the root of the git repo?
Versions:
JetBrains Rider 2019.3.1
Build #RD-193.5662.14, built on December 19, 2019
Unity 2018.4.15f1
Reproduced, thank you!
cherry-pick to 2019.3.2 https://github.com/JetBrains/resharper-unity/pull/1491
Thanks for the rapid fix! But, is there any workaround in the meantime? This is making it very hard to work with a Unity project and version control when it keeps making extra meta files everywhere, including in submodules.
@Kylotan
You may set some special gitignore rules.
You may use one of the older builds https://www.jetbrains.com/rider/download/other.html
However 2019.3.2 is planned to be released at the end of next week.
Sorry for delay. 2019.3.2 with this fix was released.
Confirmed, the issue is gone on my end. Note that after updating Rider you have to restart Unity, I guess that otherwise the plugin doesn't reload.
OK that was premature, it worked once but failed the next time when unshelving a patch with moved .metas:

My workaround is handpicking .meta files and unshelving them first, and then unshelving everything else.
@van800 This is just to let you know that we are still seeing the error in Rider 2019.3.4.
@bartlomiej-dawidow Thank you for the heads-up, somehow I missed your previous comments. It seems that you are facing some issue different from originally reported. This issue and its fix are all about .meta files outside Assets folder. It you have some different issue, please report it separately. I would be happy to investigate.
@van800 Sure: #1579
Most helpful comment
Reproduced, thank you!