Merge pull request #10 from Kepler-Workflow-Paper/author_nadrow

Author nadrow
reverts pull request merge
try to fix
Adds the latest comilation run examples
Try to resolve conficts.

Merge branch 'distribution'

Conflicts:
	graphics/test_plot.pdf
	graphics/test_plot_two1.pdf
	graphics/test_plot_two2.pdf
	open_science_paper.pdf
prep for merge with master
removes content
removes content
reverts to pre pull request merge status
Reverts master to pre pull request merge status
Changes content:

Small corrections on the readme.
Updates content:

Updates last example content.
Updates content:

Updates the example graphics and PDF to latest LaTeX run on the
document.
Changes content:

This commit changes the variable name used for the switch between an empty and
an example content filled document.
Structural changes:

Adds a new folder to the graphics path to keep the dynamically created graphics
from the R chunks. The change in the global Knitr options takes care about that
and puts all of them there. This makes it easier to clean the document with the
makefile, which from now on also cleans that dynamic folder. The commit also
moves the example content to the new path and updates the PDF file.
Updates content:

Updates examples to latest LaTeX run.
Adds content:

Adds the data folder for research data storage.
Changes layout:

This commit changes the layout of the items so they are lined up with
the headers and the text of the paper.
Updates content:

This commit updates the example content with latest LaTeX run.
Changes Layout:

Decided to roll back to the 1.5em indent of lists again. There will be
list environment to use uder the section headings soon.