shed_upload include with strip_components and '..' in paths

[peterjc]

In order to handle include source paths combining .. and strip_components, the path manipulation must be done before calculating relative paths (which drops the .. entries). The easiest way to do this seemed to me to move all the path realisation out of the RealizedFile object, thus the refactoring.

(This is a corner case I missed while working on #185)

Motivating example peterjc/pico_galaxy@1029aa9 which wasn't working as expected.

i.e. With this .shed.yml include block:

$ tail ~/repositories/pico_galaxy/tools/venn_list/.shed.yml
include:
- strip_components: 2
  source:
  - ../../tools/venn_list/README.rst
  - ../../tools/venn_list/tool_dependencies.xml
  - ../../tools/venn_list/venn_list.py
  - ../../tools/venn_list/venn_list.xml
  - ../../test-data/magic.pdf
  - ../../test-data/venn_list.tabular
  - ../../test-data/rhodopsin_proteins.fasta

Before this fix:

$ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/venn_list/ && tar -tzf shed_upload.tar.gz
cp '/tmp/tmpdjKBhQ' 'shed_upload.tar.gz'
README.rst
test-data/magic.pdf
test-data/rhodopsin_proteins.fasta
test-data/venn_list.tabular
tool_dependencies.xml
venn_list.py
venn_list.xml

With this fix:

$ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/venn_list/ && tar -tzf  shed_upload.tar.gz
cp '/tmp/tmpvOdqFl' 'shed_upload.tar.gz'
test-data/magic.pdf
test-data/rhodopsin_proteins.fasta
test-data/venn_list.tabular
tools/venn_list/README.rst
tools/venn_list/tool_dependencies.xml
tools/venn_list/venn_list.py
tools/venn_list/venn_list.xml

Note: The test case may well be not quite as @jmchilton would write it - I was attempting to model it after the existing complex repository examples.

[jmchilton]

Wonderful @peterjc - this is great! I will do a new release with this today.