moves markdown cheat sheet to methods and image to discussion

chapter-1-introduction.md

 Introduction
 ============
 
-This introduction serves as a Markdown Cheat Sheet. The header above is a first
-level header.
+This document is a template for how to use **pandoc** to write texts. You can
+find a (**pandoc**-flavored) Markdown Cheat Sheet in the **Methods** chapter.
+The **Results** and **Discussion** chapters include useful ways on how to
+include external files into the document.
 
-Header Level
-------------
+See the `README.md` file for more information on how to build this document.
 
-This is a second level header.
-
-### Third Level Header
-
-You can also just use the hashes syntax instead of the underlines with dashes
-or equals signs. Add more hashes for deeper nesting.
-
-Paragraphs
-----------
-
-To add a paragraph simply write some text and then add two newlines to separate
-this paragraph from another one.
-
-Like this. Note that it is useful to use hard line wrapping. The alternative,
-soft wrapping, is when your editor wraps the lines only visually. Consider
-using your editor to automatically re-wrap paragraphs for you.
-
-Emphasis
---------
-
-You can emphasize like this:
-
-- *italics* or _italics_
-- **bold** or __bold__
-- ~~strike-through~~
-- `verbatim`
-
-Quoting
--------
-
-> This is a block quote.
->
-> And another paragraph.
-
-Lists
------
-
-- list
-- are
-- very
-- simple
-
-1.  ordered
-1.  is also
-1.  possible
-
--   this is a list item
-
-    with another paragraph
-
-Hyperlinks
-----------
-
-You can find the complete **pandoc** Markdown documentation
-[here](https://pandoc.org/MANUAL.html#pandocs-markdown).
-
-You can also structure this a bit more [differently][pandoc] and provide the
-list of links later or at the end of the file.
-
-[pandoc]: https://pandoc.org/MANUAL.html#pandocs-markdown
-
-Footnotes
----------
-
-You can footnotes to your text like this.[^1]
-
-[^1]: This looks just like hyperlinks!
-
-Bibliography
-------------
-
-This one is often cited [see @WatsonCrick1953].
-
-Images
-------
-
-![The image caption goes here.](img/git-remote-commands.svg)
-
-Syntax Highlighting
--------------------
-
-This is a verbatim text block, also called fenced code block:
-
-```
-This is a so-called fenced block.
-Everything inside will be translated verbatim.
-No **emphasis** works here.
-A fixed-width font is used to display these blocks.
-```
-
-This code block has no syntax highlighting. To enable syntax highlighting, add
-the language to the starting fence:
-
-```r
-# you can also add code blocks with syntax highlighting
-# this is an R code snippet
-# specify the language at the starting fence
-
-# using fread is much faster
-library(data.table)
-table <- fread('example.csv')
-
-# than using read.csv
-table <- read.csv('example.csv')
-```
-
-Tables
-------
-
-See the **Results** chapter below for some examples.
-
-LaTeX if you need it
---------------------
-
-As you can see, Markdown is very simple. If you need more advanced
-type-setting, you can always fall back to using \LaTeX. You can use inline
-formulas like $a^2 + b^2 = c^2$. You can also use them standalone:
-
-$$a^2 + b^2 = c^2$$
-
-You can do the same with tables and pretty much else.
+> May the source be with you!

chapter-2-methods.md

 Methods
 =======
+
+This chapter shows how to use Markdown. The header above is a first level
+header.
+
+Header Level
+------------
+
+This is a second level header.
+
+### Third Level Header
+
+You can also just use the hashes syntax instead of the underlines with dashes
+or equals signs. Add more hashes for deeper nesting.
+
+Paragraphs
+----------
+
+To add a paragraph simply write some text and then add two newlines to separate
+this paragraph from another one.
+
+Like this. Note that it is useful to use hard line wrapping. The alternative,
+soft wrapping, is when your editor wraps the lines only visually. Consider
+using your editor to automatically re-wrap paragraphs for you.
+
+Emphasis
+--------
+
+You can emphasize like this:
+
+- *italics* or _italics_
+- **bold** or __bold__
+- ~~strike-through~~
+- `verbatim`
+
+Quoting
+-------
+
+> This is a block quote.
+>
+> And another paragraph.
+
+Lists
+-----
+
+- list
+- are
+- very
+- simple
+
+1.  ordered
+1.  is also
+1.  possible
+
+-   this is a list item
+
+    with another paragraph
+
+Hyperlinks
+----------
+
+You can find the complete **pandoc** Markdown documentation
+[here](https://pandoc.org/MANUAL.html#pandocs-markdown).
+
+You can also structure this a bit more [differently][pandoc] and provide the
+list of links later or at the end of the file.
+
+[pandoc]: https://pandoc.org/MANUAL.html#pandocs-markdown
+
+Footnotes
+---------
+
+You can add footnotes to your text like this.[^1]
+
+[^1]: This looks just like hyperlinks!
+
+Bibliography
+------------
+
+This one is often cited [see @WatsonCrick1953].
+
+Images
+------
+
+See the **Discussion** chapter below (in the final PDF) or the
+`chapter-4-discussion.md` file for some examples.
+
+Syntax Highlighting
+-------------------
+
+This is a verbatim text block, also called fenced code block:
+
+```
+This is a so-called fenced block.
+Everything inside will be translated verbatim.
+No **emphasis** works here.
+A fixed-width font is used to display these blocks.
+```
+
+This code block has no syntax highlighting. To enable syntax highlighting, add
+the language to the starting fence:
+
+```r
+# you can also add code blocks with syntax highlighting
+# this is an R code snippet
+# specify the language at the starting fence
+
+# using fread is much faster
+library(data.table)
+table <- fread('example.csv')
+
+# than using read.csv
+table <- read.csv('example.csv')
+```
+
+Tables
+------
+
+See the **Results** chapter below (in the final PDF) or the
+`chapter-3-results.md` file for some examples.
+
+LaTeX if you need it
+--------------------
+
+As you can see, Markdown is very simple. If you need more advanced
+type-setting, you can always fall back to using \LaTeX. You can use inline
+formulas like $a^2 + b^2 = c^2$. You can also use them standalone:
+
+$$a^2 + b^2 = c^2$$
+
+You can do the same with tables and pretty much else.

chapter-4-discussion.md

 Discussion
 ==========
+
+![This is the image caption. This image shows how git remotes
+work.](img/git-remote-commands.svg)