File integrity and local api scripts location

I am adding some api scripts to the Matomo server
It seems logical to place these in a sub-directory of the Matomo installation - which is the DocumentRoot
However, I do this the Sytem Check complains

Files were found in your Matomo, but we didn’t expect them.

Are there any implications by havins a sub-directory there (would an upgrade remove them?)
What is the recommended location for such scripts?
Thanks for your feedback

This should not introduce any problems, except the error notification in the system check. However, there should not be any “foreign” scripts / code added under the matomo webroot folder. Updating via the one-click updater should work, but other update methods (e.g. replace the whole directory) will delete the folder and scripts. To make this cleaner, 3rd party scripts should live in their own vHost or in a directoy structure beside the matomo webroot.

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