Private files need a separate migration from public files, because their source path will differ. Haven't looked too closely, but this probably requires core support - like, an option on the file source plugin to select only public or only private files.
The hard part here is the UX - from comment #3 below:
In Drupal 6, the files directory is either all public or private, so there's only one file directory configuration to worry about. In Drupal 7 you can have a public file directory and and private file directory (and the latter isn't necessarily in the docroot), so we need to configure two file migration processes, one for each. In our current workflow, we don't know whether we're dealing with a D6 or D7 site (and thus whether we need to prompt for a private file directory) until submitting the credential form. How do we deal with this?
- Instead of auto-detecting the source version, prompt for it on the credentials form, and use ajax to show/hide the private directory prompt (submitting the form would still detect the version and throw an error if it didn't match the selected version).
- Have a separate page after the credentials form for file configuration, which can easily have one or two file directory prompts as appropriate. And perhaps other version-specific prompts as well...
- Other ideas?