planemo shed_build does not use the .shed.yml manifest

Sample output using a tool from https://github.com/peterjc/pico_galaxy as a example:

```
$ planemo --version
planemo, version 0.24.0.dev0
$ planemo shed_build tools/align_back_trans/
Created: /mnt/galaxy/repositories/pico_galaxy/tools/align_back_trans.tar.gz
$ tar -tzf tools/align_back_trans.tar.gz
#README.rst#
.shed.yml
README.rst
README.rst~
align_back_trans.py
align_back_trans.xml
align_back_trans.xml~
tool_dependencies.xml
tool_dependencies.xml~
```

This has apparently simply zipped up all the files in the `tools/align_back_trans/` folder, including editor temp files, with no regard to the `.shed.yml` instructions.

In this case I use an explicit white-list approach:

```
$ more tools/align_back_trans/.shed.yml
name: align_back_trans
owner: peterjc
homepage_url: https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
remote_repository_url: https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
description: Thread nucleotides onto a protein alignment (back-translation)
long_description: |
Takes an input file of aligned protein sequences (typically FASTA or Clustal
format), and a matching file of unaligned nucleotide sequences (FASTA format,
using the same identifiers), and threads the nucleotide sequences onto the
protein alignment to produce a codon aware nucleotide alignment - which can
be viewed as a back translation.
categories:
- Fasta Manipulation
- Sequence Analysis
type: unrestricted
include:
- strip_components: 2
source:
- ../../test-data/demo_nuc_align.fasta
- ../../test-data/demo_nucs.fasta
- ../../test-data/demo_nucs_trailing_stop.fasta
- ../../test-data/demo_prot_align.fasta
- ../../tools/align_back_trans/README.rst
- ../../tools/align_back_trans/align_back_trans.py
- ../../tools/align_back_trans/align_back_trans.xml
- ../../tools/align_back_trans/tool_dependencies.xml
```

Expected output should match `planemo shed_upload --tar_only` as shown below:

```
$ planemo shed_upload -t work_around --tar_only ~/repositories/pico_galaxy/tools/align_back_trans/
cp '/tmp/tmpkWdWUM' 'shed_upload.tar.gz'
$ tar -tzf shed_upload.tar.gz
test-data/demo_nuc_align.fasta
test-data/demo_nucs.fasta
test-data/demo_nucs_trailing_stop.fasta
test-data/demo_prot_align.fasta
tools/align_back_trans/README.rst
tools/align_back_trans/align_back_trans.py
tools/align_back_trans/align_back_trans.xml
tools/align_back_trans/tool_dependencies.xml
```

(Note I had to specify a target tool shed, see #410 for details)