
Pictures not displaying under 'Photos'
If I upload a new picture using the web UI, it shows up under 'My Files' and Photos, correctly
If I copy an existing folder on the server to a user's folder (user-files/chris/), they show up under 'My Files', but not Photos.
Is there any process I need to run to scan the files as photos?
Answer

It is as easy as right-clicking the folder in FileRun's user interface, go to "More options" and select "Index files". The option is available only to the FileRun superuser though.
To do it from the command line:
cd cron
php metadata_update_file_type.php /path/to/folder/
Will assign a FileRun metadata file type (will mark the files as Photo, Image, Audio, etc.) and automatically extract metadata for the appropriate types (for example: image width, height, creation date, and the rest of the Exif/IPTC/XMP data for image files), for all files found at the specified /path/to/folder/
path.

I suggest checking your photo files and see if they have been assigned the proper metadata file type and if data has been extracted from them. You might be missing Exif support from your PHP installation.

2 questions:
Are some of these cli tools meant to run regularly in a cron? I am using the docker image afian/filerun, which does not have a cron implementation installed
As the superuser, how can I access a different user's files in order to run the 'Index files' option?

You can run the command lines using a cron job if you want them to run regularly. This page also includes guidance on how to add cron to the Docker version, relatively easy: http://docs.filerun.com/docker-tika
As for the last question, you can set the other user's home folders inside the superuser's home folder. That would be the only option currently, for using the UI indexing option.
Customer support service by UserEcho
It is as easy as right-clicking the folder in FileRun's user interface, go to "More options" and select "Index files". The option is available only to the FileRun superuser though.
To do it from the command line:
cd cron
php metadata_update_file_type.php
/path/to/folder/