Caveats

What it cannot see, and what a copy cannot carry.

LimitWhat it means
What doctor cannot seeOnly git's own records and two file formats that write their own path. Anything else that points into a directory, including a line in a shell profile or a process whose working directory is inside it, is invisible to the report.
What a clone cannot carryAbsolute paths inside files that doctor does not know the format of. A compiled artifact with a build path baked into it, a database with a stored data directory, a lockfile that recorded where it ran. They are copied faithfully and they still name the original.
Which filesystems can share blocksA filesystem missing from this table is measured like any other, so the answer comes from the probe.