The same question popped up in the Atom forums some weeks back. There’s now a good explanation on the issue on their FAQ page.
With macOS 10.14 Mojave, Apple introduced new privacy protections similar to the existing protections found in iOS. Whenever an application attempts to access the files inside certain newly-protected directories, macOS asks the user whether they want to allow the application to access the content in those directories. These new privacy protections apply to the directories that contain your calendars, contacts, photos, mail, messages, and Time Machine backups.
…
This commonly occurs when you open your home directory (~
) inside Atom and run a command that examines all files and directories beneath your home directory.
…
In addition to containing the files you’re intending to edit inside Atom, your home directory also contains your files that have new OS-level protections in Mojave:
Calendar files (~/Library/Calendars
)
Contacts files (~/Library/Application\ Support/AddressBook
)
Mail files (~/Library/Mail
)
Photos files (~/Pictures/Photos\ Library.photoslibrary
)
Before letting Atom read these files, Mojave is understandably asking whether you want Atom to be able to access this personal data.