test: rearrange the test corpus into subfolders, fix tests

We will need this for improved folder search tests, but having some
folders should exercise our code paths better anyway.

Modify the relevant test accordingly to make it pass.

This reorganization triggers a bug in the test suite, namely that it
expects the output of --output=files to be in a certain order. So we
add the fix for that into the same commit.

This mainly involves sorting, although the case --duplicate=$n
requires more subtlety.