planemo uploads to the Tool Shed include unwanted files

It seems planemo is uploading unwanted files to the Tool Shed with individual tool uploads. In some cases it uploads multiple tools from a demultiplexed git repository into a single tool repository, while in other cases it uploads unwanted files from other tools.

The individual ImageJ2 tools are demultiplexed in here: https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2
Planemo uploaded each of these tools to the TTS, including every ImageJ2 tool in each individual repo:

```
Repository 'imagej2_adjust_threshold_binary' revision c05d862ac753 (repository tip)
Contents:
imagej2_adjust_threshold_binary.py
imagej2_adjust_threshold_binary.xml
imagej2_adjust_threshold_binary_jython_script.py
imagej2_analyze_particles_binary.py
imagej2_analyze_particles_binary_jython_script.py
imagej2_analyze_skeleton.py
imagej2_analyze_skeleton_jython_script.py
...
```

On the MTS, the meme tool repo contains the fimo tool's Python script:

```
Repository 'meme_meme' revision 487ce3fa1822 (repository tip)
Contents:
all_fasta.loc.sample
fimo_wrapper.py
meme.xml
test-data/
tool_data_table_conf.xml.sample
tool_dependencies.xml
```

There are other similar examples on both the TTS and MTS.