planemo shed_diff -r breaks if sub-directory not recognised

This folder is a very early work in progress, with no `.shed.yml` and no `*.xml` file either. As expected, `planemo shed_diff` fails (although not cleanly):

```
$ ls -1 ~/repositories/pico_galaxy/tools/seq_concatenate/
seq_concatenate.py
$ planemo shed_diff --shed_target testtoolshed ~/repositories/pico_galaxy/tools/seq_concatenate/
Unable to find repository id, cannot download.
Traceback (most recent call last):
...
Exception: Unable to find repository id, cannot download.
```

The problem is that this also happens in recursive mode. It should report this, but keep going:

```
$ planemo shed_diff --shed_target testtoolshed -r ~/repositories/pico_galaxy/tools/
...

...
Unable to find repository id, cannot download.
Traceback (most recent call last):
...
Exception: Unable to find repository id, cannot download.
```

Start by reproducing the issue with `planemo shed_diff --shed_target testtoolshed -r` against a directory containing an unrecognised sub-directory such as `seq_concatenate/`. Trace the recursive `shed_diff` entry point and the repository lookup that raises the exception; done means reporting the missing repository while continuing to process the remaining directories.

Written by the indexing model from the issue text.