planemo shed_diff reports deprecated repositories do not exist

eg using https://github.com/peterjc/pico_galaxy under Linux

```
$ planemo --version
planemo, version 0.45.0.dev0
```

```
$ planemo shed_diff -t toolshed -r tools/
...
Diffing repository [effectivet3]
wget -q -O - 'https://toolshed.g2.bx.psu.edu/repository/download?repository_id=26f26c7aa084d325&changeset_revision=default&file_type=gz' | tar -xzf - -C /tmp/tool_shed_diff_VVhG7d/_toolshed_ --strip-components 1
mkdir "/tmp/tool_shed_diff_VVhG7d/_workingdir_"; tar -xzf "/tmp/tmpe5soP6" -C "/tmp/tool_shed_diff_VVhG7d/_workingdir_"; rm -rf /tmp/tmpe5soP6
cd "/tmp/tool_shed_diff_VVhG7d"; diff -r _workingdir_ _toolshed_ >> '/tmp/tmp13STNw'
shed_diff: Repository [fasta_filter_by_id] does not exist in the targeted Tool Shed.
shed_diff: Repository [fastq_filter_by_id] does not exist in the targeted Tool Shed.
shed_diff: Repository [fastq_pair_names] does not exist in the targeted Tool Shed.
Diffing repository [fastq_paired_unpaired]
...
```

Right now ``fastq_pair_names`` is currently just on the Test Tool Shed, so the message is correct: http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_pair_names vs http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_pair_names

Here ``fasta_filter_by_id`` and ``fastq_filter_by_id`` do exist, but are deprecated:
* http://toolshed.g2.bx.psu.edu/view/peterjc/fasta_filter_by_id
* http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_filter_by_id

My use case for running shed-diff recursively like this is to check for any tools I need to update on the main repository. When a tool has been deprecated I would ideally like it to be checked for diffs, but reported as deprecated without checks would be fine.