add --out argument for tap package download

Adds the optional --out parameter for package download

If several --out parameters are specified, they are assumed to have the same order as the input Packages being downloaded. If any --out parameters are specified, all downloads with no --out parameter specified are placed in the same directory as the last --out with their default names.

While testing the feature, I discovered a bug which prevented our FileRepository from working if it doesn't have read permissions to any of its subdirectories. It now skips directories that it can't read and shows a debug warning.

Closes #379 (closed) Closes #390 (closed)