Make --output-dir work on cross-device destinations

[cscheid]

Closes #2671.

[cscheid]

This is going to be quite obnoxious to test in CI (especially across operating systems), so I didn't add any regression tests.

[cscheid]

For the record, I tested this on macOS the following way:

$ mkdir test
$ sudo mount_tmpfs test
$ echo Hi > test.qmd
$ quarto render test.qmd --to markdown --output-dir test