Update material to reflect new directory structure

Fix swcarpentry#1225.

_episodes/02-filedir.md

@@ -377,8 +377,7 @@ $ ls -F Desktop/shell-lesson-data
 {: .language-bash}
 
 ~~~
-creatures/          molecules/          notes.txt           solar.pdf
-data/               north-pacific-gyre/ pizza.cfg           writing/
+exercise-data/  north-pacific-gyre/
 ~~~
 {: .output}
 
@@ -400,15 +399,18 @@ use the following series of commands to get there:
 ~~~
 $ cd Desktop
 $ cd shell-lesson-data
-$ cd data
+$ cd exercise-data
 ~~~
 {: .language-bash}
 
 These commands will move us from our home directory into our Desktop directory, then into
-the `shell-lesson-data` directory, then into the `data` directory. You will notice that `cd` doesn't print anything. This is normal. Many shell commands will not output anything to the screen when successfully executed. But if we run `pwd` after it, we can see that we are now
-in `/Users/nelle/Desktop/shell-lesson-data/data`.
+the `shell-lesson-data` directory, then into the `exercise-data` directory.
+ You will notice that `cd` doesn't print anything. This is normal.
+Many shell commands will not output anything to the screen when successfully executed.
+But if we run `pwd` after it, we can see that we are now
+in `/Users/nelle/Desktop/shell-lesson-data/exercise-data`.
 If we run `ls -F` without arguments now,
-it lists the contents of `/Users/nelle/Desktop/shell-lesson-data/data`,
+it lists the contents of `/Users/nelle/Desktop/shell-lesson-data/exercise-data`,
 because that's where we now are:
 
 ~~~
@@ -417,7 +419,7 @@ $ pwd
 {: .language-bash}
 
 ~~~
-/Users/nelle/Desktop/shell-lesson-data/data
+/Users/nelle/Desktop/shell-lesson-data/exercise-data
 ~~~
 {: .output}
 
@@ -427,8 +429,7 @@ $ ls -F
 {: .language-bash}
 
 ~~~
-amino-acids.txt   elements/     pdb/	        salmon.txt
-animals.txt       morse.txt     planets.txt     sunspot.txt
+animal-counts/  backup/  creatures/  numbers.txt  project/  proteins/  writing/
 ~~~
 {: .output}
 
@@ -487,8 +488,7 @@ $ ls -F -a
 {: .language-bash}
 
 ~~~
-./   .bash_profile  data/       north-pacific-gyre/  pizza.cfg  thesis/
-../  creatures/     molecules/  notes.txt            solar.pdf  writing/
+./  ../  exercise-data/  north-pacific-gyre/
 ~~~
 {: .output}
 
@@ -552,14 +552,14 @@ $ pwd
 {: .output}
 
 It turns out that `cd` without an argument will return you to your home directory,
-which is great if you've gotten lost in your own filesystem.
+which is great if you've got lost in your own filesystem.
 
-Let's try returning to the `data` directory from before. Last time, we used
+Let's try returning to the `exercise-data` directory from before. Last time, we used
 three commands, but we can actually string together the list of directories
-to move to `data` in one step:
+to move to `exercise-data` in one step:
 
 ~~~
-$ cd Desktop/shell-lesson-data/data
+$ cd Desktop/shell-lesson-data/exercise-data
 ~~~
 {: .language-bash}
 
@@ -581,7 +581,7 @@ the root of the file system, so it always refers to exactly one directory,
 no matter where we are when we run the command.
 
 This allows us to move to our `shell-lesson-data` directory from anywhere on
-the filesystem (including from inside `data`). To find the absolute path
+the filesystem (including from inside `exercise-data`). To find the absolute path
 we're looking for, we can use `pwd` and then extract the piece we need
 to move to `shell-lesson-data`.
 
@@ -591,7 +591,7 @@ $ pwd
 {: .language-bash}
 
 ~~~
-/Users/nelle/Desktop/shell-lesson-data/data
+/Users/nelle/Desktop/shell-lesson-data/exercise-data
 ~~~
 {: .output}
 
@@ -627,9 +627,9 @@ Run `pwd` and `ls -F` to ensure that we're in the directory we expect.
 > ~~~
 > {: .language-bash}
 >
-> Then `cd` into the `creatures` directory
+> Then `cd` into the `exercise-data/creatures` directory
 > ~~~
-> $ cd creatures
+> $ cd exercise-data/creatures
 > ~~~
 > {: .language-bash}
 >
@@ -639,7 +639,7 @@ Run `pwd` and `ls -F` to ensure that we're in the directory we expect.
 > ~~~
 > {: .language-bash}
 > you'll see you're back in `~/Desktop/shell-lesson-data`.
-> Run `cd -` again and you're back in `~/Desktop/shell-lesson-data/creatures`
+> Run `cd -` again and you're back in `~/Desktop/shell-lesson-data/exercise-data/creatures`
 {: .callout}
 
 > ## Absolute vs Relative Paths
@@ -756,13 +756,11 @@ For example, `ls -s` will display the size of files and directories alongside th
 while `ls -S` will sort the files and directories by size, as shown below:
 
 ~~~
-$ ls -s Desktop/shell-lesson-data/data
-total 116
- 4 amino-acids.txt   4 animals.txt   4 morse.txt  12 planets.txt  76 sunspot.txt
- 4 animal-counts     4 elements      4 pdb         4 salmon.txt
+$ ls -s Desktop/shell-lesson-data/exercise-data/
+total 28
+ 4 animal-counts   4 creatures  12 numbers.txt   4 proteins   4 writing
 $ ls -S Desktop/shell-lesson-data/data
-sunspot.txt  animal-counts  pdb        amino-acids.txt  salmon.txt
-planets.txt  elements       morse.txt  animals.txt
+animal-counts  creatures  proteins  writing  numbers.txt
 ~~~
 {: .output}
 
@@ -791,24 +789,9 @@ First,
 she creates a directory called `north-pacific-gyre`
 (to remind herself where the data came from).
 Inside that,
-she creates a directory called `2012-07-03`,
-which is the date she started processing the samples.
-She used to use names like `conference-paper` and `revised-results`,
-but she found them hard to understand after a couple of years.
-(The final straw was when she found herself creating
-a directory called `revised-revised-results-3`.)
-
-> ## Sorting Output
->
-> Nelle names her directories 'year-month-day',
-> with leading zeroes for months and days,
-> because the shell displays file and directory names in alphabetical order.
-> If she used month names,
-> December would come before July;
-> if she didn't use leading zeroes,
-> November ('11') would come before July ('7'). Similarly, putting the year first
-> means that June 2012 will come before June 2013.
-{: .callout}
+she creates a directory called `data`,
+which will contains the data files from the assay machine.
+
 
 Each of her physical samples is labelled according to her lab's convention
 with a unique ten-character ID,
@@ -820,11 +803,14 @@ Since the assay machine's output is plain text,
 she will call her files `NENE01729A.txt`, `NENE01812A.txt`, and so on.
 All 1520 files will go into the same directory.
 
+She also creates a `scripts` directory to contain the processing script `goostats.sh`
+written by her supervisor, and any new scripts she will write for this project.
+
 Now in her current directory `shell-lesson-data`,
 Nelle can see what files she has using the command:
 
 ~~~
-$ ls north-pacific-gyre/2012-07-03/
+$ ls north-pacific-gyre/
 ~~~
 {: .language-bash}
 
@@ -845,13 +831,10 @@ $ ls north-pacific-gyre/
 ~~~
 {: .language-bash}
 
-If she presses <kbd>Tab</kbd> again,
-Bash will add `2012-07-03/` to the command,
-since it's the only possible completion.
 Pressing <kbd>Tab</kbd> again does nothing,
-since there are 19 possibilities;
-pressing <kbd>Tab</kbd> twice brings up a list of all the files,
-and so on.
+since there are 2 possibilities;
+pressing <kbd>Tab</kbd> twice brings up a list of all the directories.
+Nelle can select the `data` directory by typing <kbd>D</kbd> and pressing <kbd>Tab</kbd> again.
 This is called **tab completion**,
 and we will see it in many other tools as we go on.
 

_episodes/03-create.md

@@ -25,9 +25,12 @@ keypoints:
 We now know how to explore files and directories,
 but how do we create them in the first place?
 
+In this episode we will learn about creating and moving files and directories,
+using the `exercise-data/writing` directory as an example.
+
 ### Step one: see where we are and what we already have
-Let's go back to our `shell-lesson-data` directory on the Desktop
-and use `ls -F` to see what it contains:
+We should still be in the `shell-lesson-data` directory on the Desktop,
+which we can checking using:
 
 ~~~
 $ pwd
@@ -39,13 +42,19 @@ $ pwd
 ~~~
 {: .output}
 
+Next we'll move to the `exercise-data/writing` directory and see what it contains:
+~~~
+$ cd `exercise-data/writing`
+~~~
+{:  .language-bash}
+
 ~~~
 $ ls -F
 ~~~
 {: .language-bash}
 
 ~~~
-creatures/  data/  molecules/  north-pacific-gyre/  notes.txt  pizza.cfg  solar.pdf  writing/
+haiku.txt  LittleWomen.txt
 ~~~
 {: .output}
 
@@ -71,7 +80,7 @@ $ ls -F
 {: .language-bash}
 
 ~~~
-creatures/  data/  molecules/  north-pacific-gyre/  notes.txt  pizza.cfg  solar.pdf  thesis/  writing/
+haiku.txt  LittleWomen.txt  thesis/
 ~~~
 {: .output}
 
@@ -86,25 +95,25 @@ Note that `mkdir` is not limited to creating single directories one at a time.
 The `-p` option allows `mkdir` to create a directory with nested subdirectories in a single operation:
 
 ~~~
-$ mkdir -p project/data project/results
+$ mkdir -p ../project/data ../project/results
 ~~~
 {: .language-bash}
 
 The `-R` option to the `ls` command will list all nested subdirectories within a directory.
 Let's use `ls -FR` to recursively list the new directory hierarchy we just created in the `project` directory:
 
 ~~~
-$ ls -FR project
+$ ls -FR ../project
 ~~~
 {: .language-bash}
 
 ~~~
-project/:
+../project/:
 data/  results/
 
-project/data:
+../project/data:
 
-project/results:
+../project/results:
 ~~~
 {: .output}
 
@@ -287,10 +296,10 @@ draft.txt
 {: .callout}
 
 ## Moving files and directories
-Returning to the `shell-lesson-data` directory,
+Returning to the `shell-lesson-data/writing` directory,
 
 ```
-cd ~/Desktop/shell-lesson-data/
+cd ~/Desktop/shell-lesson-data/writing
 ```
 {: .language-bash}
 
@@ -536,7 +545,7 @@ quotations.txt
 
 ## Removing files and directories
 
-Returning to the `shell-lesson-data` directory,
+Returning to the `shell-lesson-data/writing` directory,
 let's tidy up this directory by removing the `quotes.txt` file we created.
 The Unix command we'll use for this is `rm` (short for 'remove'):
 
@@ -618,13 +627,13 @@ Oftentimes one needs to copy or move several files at once. This can be done by
 
 > ## Copy with Multiple Filenames
 >
-> For this exercise, you can test the commands in the `shell-lesson-data/data` directory.
+> For this exercise, you can test the commands in the `shell-lesson-data/exercise-data` directory.
 >
 > In the example below, what does `cp` do when given several filenames and a directory name?
 >
 > ~~~
 > $ mkdir backup
-> $ cp amino-acids.txt animals.txt backup/
+> $ cp creatures/minotaur.dat creatures/unicorn.dat backup/
 > ~~~
 > {: .language-bash}
 >
@@ -635,11 +644,11 @@ Oftentimes one needs to copy or move several files at once. This can be done by
 > ~~~
 > {: .language-bash}
 > ~~~
-> amino-acids.txt  animals.txt  backup/  elements/  morse.txt  pdb/  planets.txt  salmon.txt  sunspot.txt
+> amino-acids.txt  animals.csv  backup/  elements/  morse.txt  pdb/  planets.txt  salmon.txt  sunspot.txt
 > ~~~
 > {: .output}
 > ~~~
-> $ cp amino-acids.txt animals.txt morse.txt
+> $ $ cp creatures/minotaur.dat creatures/unicorn.dat backup/ creatures/basilisk.dat
 > ~~~
 > {: .language-bash}
 >
@@ -651,7 +660,7 @@ Oftentimes one needs to copy or move several files at once. This can be done by
 > > name as the last argument.
 > >
 > > ```
-> > cp: target ‘morse.txt’ is not a directory
+> > cp: target 'creatures/basilisk.dat' is not a directory
 > > ```
 > > {: .output}
 > {: .solution}
@@ -662,7 +671,7 @@ Oftentimes one needs to copy or move several files at once. This can be done by
 > ## Wildcards
 >
 > `*` is a **wildcard**, which matches zero or more  characters.
-> Let's consider the `shell-lesson-data/molecules` directory:
+> Let's consider the `shell-lesson-data/exercise-data/proteins` directory:
 > `*.pdb` matches `ethane.pdb`, `propane.pdb`, and every
 > file that ends with '.pdb'. On the other hand, `p*.pdb` only matches
 > `pentane.pdb` and `propane.pdb`, because the 'p' at the front only
@@ -691,7 +700,7 @@ Oftentimes one needs to copy or move several files at once. This can be done by
 
 > ## List filenames matching a pattern
 >
-> When run in the `molecules` directory, which `ls` command(s) will
+> When run in the `proteins` directory, which `ls` command(s) will
 > produce this output?
 >
 > `ethane.pdb   methane.pdb`