* Which daemon actually runs the remote file-transfer plugins? My guess would be the starter.
Correct.
* The standard htcondor file transfer from the AP's local FS runs via the shadow to the starter, correct? As in both at the start of a job but also the other way during clean-up?
The shadow sends files to the starter for input transfer, and vice-versa for checkpoints and output files.
* If one has configured for a shared file system, the job itself should have direct access to files from that NFS/Lustre/BeeGFS/whatever system therefore doesn't need any daemon process mediator.
Correct.
* Which daemon destroys the sandbox, the starter or the startd?
Both. The starter tries, and then the startd checks (and tries again if it has to).
-- ToddM