Add debugging notes about Git and line endings

Import style for slides from https://github.com/swcarpentry/slideshows

Excluding unwanted files from build

(DO NOT CLONE) added adapted version of motivation.md that uses the pandoc slide generator and the new swc style

don't clone unless you know what you're doing (this commit will probably disappear)

- the "--slide-level 2" allows to generate consistent html structure
- one should only use "##" but never "#" for now

It has been produced and can be updated with the following commands:

    git clone https://github.com/twitwi/deck.js-theme-builder tmpbuilder
    cd tmpbuilder/
    make
    cd ..
    cp tmpbuilder/software-carpentry.css css/swc-slides.css
    mkdir css/local-fonts
    cp tmpbuilder/local-fonts/zhcz-_WihjSQC0oHJ9TCYBsxEYwM7FgeyaSgU71cLG0.woff css/local-fonts/

It has been generated (and can be updated) using the following commands:

    git clone https://github.com/twitwi/deck.js tmpdeck
    node ./tmpdeck/extensions/bundle-maker/make-packed.js "profile-5" js/deckjs-custom.js
    sed -i -e 's@/home/.*/tmpdeck//*@..../@g' js/deckjs-custom.js

Update LAYOUT for changes from #103

Change filters since classes must be explicit

Add examples of links to part of our lessons

Add classes

All classes **must** be explicit because this will make easy
to translate the lessons.

Improving support for R Markdown.

1.  Adding `tools/chunk-options.R` with support for Pandoc-based conversion of R Markdown to plain Markdown.
2.  Modifying `Makefile` to handle any R Markdown files that are present.

Changes have been checked by @jdblischak in the `r-novice-inflammation` project.