What a copy does not carry
Dependencies, build output and secrets are the three things you must deliberately not copy, and deliberately replace.
Copying an application directory is a good way to move an application and a terrible way to move a running one.
Installed dependencies are compiled for the machine they were installed on. Build output describes the environment it was built in. And the secrets file is the one thing that must change, because it names the database, the host and the addresses the new machine will use.
So exclude all three from the copy, and then say so. An exclusion you have accounted for is a decision. An exclusion nobody wrote down is a missing file, and the first person to notice will be a customer.