Merge branch 'updates_bow' into 'master'

Updates bow

Slight delay because yesterday some things took more time than I predicted..

But I think the tips presentation is ready now :). I added the git-prompt.sh file (which comes with a git install) to the repository just to be sure we have a backup in case the file is not available in the laptops.

Other than that, I skipped the autocrlf / safecrlf config since it seems more complicated for first-time git users. Instead, I added some slides about `git add --patch` for selective commits of line changes, which I think is more useful (and easier to grasp).

Anyway, comments are welcomed.

basics/basics.tex

@@ -2,7 +2,7 @@
 
 \title{Git Basics}
 \providecommand{\myConference}{Git course}
-\providecommand{\myDate}{Monday, October 14, 2013}
+\providecommand{\myDate}{Monday, June 23, 2014}
 \author{Jeroen F. J. Laros}
 \providecommand{\myGroup}{Leiden Genome Technology Center}
 \providecommand{\myDepartment}{Department of Human Genetics}
@@ -39,6 +39,7 @@
   \bigskip
  
   \begin{lstlisting}[language=none, caption=Make a new repository.]
+    $ cd ~/projects
     $ git init
     Initialized empty Git repository in <path>/.git/
   \end{lstlisting}
@@ -186,6 +187,43 @@
   \end{lstlisting}
 \end{frame}
 
+\begin{frame}[fragile]
+  \frametitle{Undoing changes.}
+
+  Keep in mind that ``\bt{git reset}'' by default sets a staged file back to unstaged.
+  \begin{lstlisting}[language=none, caption=Unstage a file.]
+    $ git reset README
+    $ git status
+    # Changes not staged for commit:
+    #       modified:   README
+  \end{lstlisting}
+  \bigskip
+  \pause
+
+  To discard all changes in an unstaged file, you can use ``\bt{git checkout}''
+  \begin{lstlisting}[language=none, caption=Discarding changes.]
+    $ git checkout -- .
+    $ git status
+    nothing to commit, working directory clean
+  \end{lstlisting}
+  
+\end{frame}
+
+\begin{frame}[fragile]
+  \frametitle{Undoing changes.}
+
+  For now, let's commit our change and move on.
+  \bigskip
+
+  \begin{lstlisting}[language=none, caption=Adding a new version of a file.]
+    $ echo Second version. > README
+    $ git commit
+    $ git status
+    nothing to commit, working directory clean
+  \end{lstlisting}
+  \bigskip
+\end{frame}
+
 \begin{frame}[fragile]
   \frametitle{Viewing the history.}
 
@@ -193,8 +231,6 @@
   \bigskip
 
   \begin{lstlisting}[language=none, caption=The log of our project.]
-    $ git add README
-    $ git commit
     $ git log
     commit cc61ee7cd72590f3bebcc9e1ff3e9435c7f7dd28
     Author: J.F.J. Laros <j.f.j.laros@lumc.nl>
@@ -228,7 +264,7 @@
   \bigskip
   \pause
 
-  You can also use an unique prefix of this hash, usually six characters is
+  You can also use a unique prefix of this hash, usually six characters is
   enough.
 \end{frame}
 
@@ -341,6 +377,8 @@
 
     Zuotian Tatum
 
+    Wibowo Arindrarto
+
   \end{center}
 
   \vfill

tips/Makefile

+../presentation/Makefile
\ No newline at end of file

tips/beamerthemelumc.sty

+../presentation/beamerthemelumc.sty
\ No newline at end of file

tips/gen2phen_logo.eps

+../presentation/gen2phen_logo.eps
\ No newline at end of file

tips/lgtc_logo.eps

+../presentation/lgtc_logo.eps
\ No newline at end of file

tips/lumc_logo.eps

+../presentation/lumc_logo.eps
\ No newline at end of file

tips/lumc_logo_small.eps

+../presentation/lumc_logo_small.eps
\ No newline at end of file

tips/nbic_logo.eps

+../presentation/nbic_logo.eps
\ No newline at end of file

tips/ngi_logo.eps

+../presentation/ngi_logo.eps
\ No newline at end of file

tips/nwo_logo_en.eps

+../presentation/nwo_logo_en.eps
\ No newline at end of file

tips/pics

+../pics/
\ No newline at end of file

tips/ul_logo.eps

+../presentation/ul_logo.eps
\ No newline at end of file