diff --git a/episodes/02-numpy.md b/episodes/02-numpy.md
index ddc807281..55fa82710 100644
--- a/episodes/02-numpy.md
+++ b/episodes/02-numpy.md
@@ -218,7 +218,7 @@ It takes a bit of getting used to,
 but one way to remember the rule is that
 the index is how many steps we have to take from the start to get the item we want.
 
-![](fig/python-zero-index.svg){alt="\\"data\\" is a 3 by 3 numpy array containing row 0: \['A', 'B', 'C'\], row 1: \['D', 'E', 'F'\], androw 2: \['G', 'H', 'I'\]. Starting in the upper left hand corner, data\[0, 0\] = 'A', data\[0, 1\] = 'B',data\[0, 2\] = 'C', data\[1, 0\] = 'D', data\[1, 1\] = 'E', data\[1, 2\] = 'F', data\[2, 0\] = 'G',data\[2, 1\] = 'H', and data\[2, 2\] = 'I',in the bottom right hand corner."}
+![](fig/python-zero-index.svg){alt="'data' is a 3 by 3 numpy array containing row 0: \['A', 'B', 'C'\], row 1: \['D', 'E', 'F'\], androw 2: \['G', 'H', 'I'\]. Starting in the upper left hand corner, data\[0, 0\] = 'A', data\[0, 1\] = 'B',data\[0, 2\] = 'C', data\[1, 0\] = 'D', data\[1, 1\] = 'E', data\[1, 2\] = 'F', data\[2, 0\] = 'G',data\[2, 1\] = 'H', and data\[2, 2\] = 'I',in the bottom right hand corner."}
 
 :::::::::::::::::::::::::::::::::::::::::  callout
 
diff --git a/episodes/11-debugging.md b/episodes/11-debugging.md
index 115ec7fd1..edb7dc179 100644
--- a/episodes/11-debugging.md
+++ b/episodes/11-debugging.md
@@ -90,7 +90,7 @@ scientists tend to do the following:
   Data analysts frequently use simple visualizations to check both
   the science they're doing
   and the correctness of their code
-  (just as we did in the [opening lesson](01-numpy) of this tutorial).
+  (just as we did in the [opening lesson](02-numpy.html) of this tutorial).
   This should only be used for debugging as a last resort,
   though,
   since it's very hard to compare two visualizations automatically.
diff --git a/episodes/12-cmdline.md b/episodes/12-cmdline.md
index deb657634..d09917aad 100644
--- a/episodes/12-cmdline.md
+++ b/episodes/12-cmdline.md
@@ -704,7 +704,7 @@ main()
 
 ## Finding Particular Files
 
-Using the `glob` module introduced [earlier](04-files),
+Using the `glob` module introduced [earlier](06-files.html),
 write a simple version of `ls` that shows files in the current directory
 with a particular suffix.
 A call to this script should look like this:
diff --git a/code/Makefile b/episodes/files/code/Makefile
similarity index 100%
rename from code/Makefile
rename to episodes/files/code/Makefile
diff --git a/code/argv_list.py b/episodes/files/code/argv_list.py
similarity index 100%
rename from code/argv_list.py
rename to episodes/files/code/argv_list.py
diff --git a/code/arith.py b/episodes/files/code/arith.py
similarity index 100%
rename from code/arith.py
rename to episodes/files/code/arith.py
diff --git a/code/check.py b/episodes/files/code/check.py
similarity index 100%
rename from code/check.py
rename to episodes/files/code/check.py
diff --git a/code/count_stdin.py b/episodes/files/code/count_stdin.py
similarity index 100%
rename from code/count_stdin.py
rename to episodes/files/code/count_stdin.py
diff --git a/code/gen_inflammation.py b/episodes/files/code/gen_inflammation.py
similarity index 100%
rename from code/gen_inflammation.py
rename to episodes/files/code/gen_inflammation.py
diff --git a/code/line_count.py b/episodes/files/code/line_count.py
similarity index 100%
rename from code/line_count.py
rename to episodes/files/code/line_count.py
diff --git a/code/my_ls.py b/episodes/files/code/my_ls.py
similarity index 100%
rename from code/my_ls.py
rename to episodes/files/code/my_ls.py
diff --git a/code/python-novice-inflammation-code.zip b/episodes/files/code/python-novice-inflammation-code.zip
similarity index 100%
rename from code/python-novice-inflammation-code.zip
rename to episodes/files/code/python-novice-inflammation-code.zip
diff --git a/code/readings_01.py b/episodes/files/code/readings_01.py
similarity index 100%
rename from code/readings_01.py
rename to episodes/files/code/readings_01.py
diff --git a/code/readings_02.py b/episodes/files/code/readings_02.py
similarity index 100%
rename from code/readings_02.py
rename to episodes/files/code/readings_02.py
diff --git a/code/readings_03.py b/episodes/files/code/readings_03.py
similarity index 100%
rename from code/readings_03.py
rename to episodes/files/code/readings_03.py
diff --git a/code/readings_04.py b/episodes/files/code/readings_04.py
similarity index 100%
rename from code/readings_04.py
rename to episodes/files/code/readings_04.py
diff --git a/code/readings_05.py b/episodes/files/code/readings_05.py
similarity index 100%
rename from code/readings_05.py
rename to episodes/files/code/readings_05.py
diff --git a/code/readings_06.py b/episodes/files/code/readings_06.py
similarity index 100%
rename from code/readings_06.py
rename to episodes/files/code/readings_06.py
diff --git a/code/readings_07.py b/episodes/files/code/readings_07.py
similarity index 100%
rename from code/readings_07.py
rename to episodes/files/code/readings_07.py
diff --git a/code/readings_08.py b/episodes/files/code/readings_08.py
similarity index 100%
rename from code/readings_08.py
rename to episodes/files/code/readings_08.py
diff --git a/code/readings_09.py b/episodes/files/code/readings_09.py
similarity index 100%
rename from code/readings_09.py
rename to episodes/files/code/readings_09.py
diff --git a/code/rectangle.py b/episodes/files/code/rectangle.py
similarity index 100%
rename from code/rectangle.py
rename to episodes/files/code/rectangle.py
diff --git a/code/sys_version.py b/episodes/files/code/sys_version.py
similarity index 100%
rename from code/sys_version.py
rename to episodes/files/code/sys_version.py
diff --git a/index.md b/index.md
index 43a069cc5..153456a64 100644
--- a/index.md
+++ b/index.md
@@ -26,7 +26,7 @@ To see how effective the treatment is we would like to:
 1. Calculate the average inflammation per day across all patients.
 2. Plot the result to discuss and share with colleagues.
 
-![](fig/lesson-overview.svg "Lesson Overview"){alt='3-step flowchart shows inflammation data records for patients moving to the Analysis stepwhere a heat map of provided data is generated moving to the Conclusion step that asks thequestion, How does the medication affect patients?'}
+![](episodes/fig/lesson-overview.svg "Lesson Overview"){alt='3-step flowchart shows inflammation data records for patients moving to the Analysis stepwhere a heat map of provided data is generated moving to the Conclusion step that asks thequestion, How does the medication affect patients?'}
 
 ### Data Format
 
diff --git a/instructors/instructor-notes.md b/instructors/instructor-notes.md
index cbdb33fba..e4c7b62ed 100644
--- a/instructors/instructor-notes.md
+++ b/instructors/instructor-notes.md
@@ -20,7 +20,7 @@ arthritis treatment.
 
 We make reference in the lesson that this data is suspicious and has been
 synthetically generated in Python by the imaginary "Dr. Maverick"! The script used to generate
-the inflammation data is included as [`code/gen_inflammation.py`](code/gen_inflammation.py).
+the inflammation data is included as [`code/gen_inflammation.py`](../episodes/files/code/gen_inflammation.py).
 
 ## Overall
 
@@ -99,7 +99,7 @@ which are covered in the lesson on the shell.
 
 - NumPy methods.
   
-  We used to use NumPy array methods in the first [NumPy topic](01-numpy).
+  We used to use NumPy array methods in the first [NumPy topic](02-numpy.html).
   We switched these methods to the equivalent functions because a majority
   of instructors supported the change; see
   [PR #244](https://github.com/swcarpentry/python-novice-inflammation/pull/244)
diff --git a/learners/reference.md b/learners/reference.md
index b0b490f0a..c58db8e7d 100644
--- a/learners/reference.md
+++ b/learners/reference.md
@@ -7,15 +7,15 @@ title: 'FIXME'
 ## Glossary
 
 {:auto\_ids}
-additive color model
+[additive color model]{#additive-color-model}
 :   A way to represent colors as the sum of contributions from primary colors
 such as [red, green, and blue](#rgb).
 
-argument
+[argument]{#argument}
 :   A value given to a function or program when it runs.
 The term is often used interchangeably (and inconsistently) with [parameter](#parameter).
 
-assertion
+[assertion]{#assertion}
 :   An expression which is supposed to be true at a particular point in a program.
 Programmers typically put assertions in their code to check for errors;
 if the assertion fails (i.e., if the expression evaluates as false),
@@ -23,24 +23,24 @@ the program halts and produces an error message.
 See also: [invariant](#invariant), [precondition](#precondition),
 [postcondition](#postcondition).
 
-assign
+[assign]{#assign}
 :   To give a value a name by associating a variable with it.
 
-body
+[body]{#body}
 :   (of a function): the statements that are executed when a function runs.
 
-call stack
+[call stack]{#call-stack}
 :   A data structure inside a running program that keeps track of active function calls.
 
-case-insensitive
+[case-insensitive]{#case-insensitive}
 :   Treating text as if upper and lower case characters of the same letter were the same.
 See also: [case-sensitive](#case-sensitive).
 
-case-sensitive
+[case-sensitive]{#case-sensitive}
 :   Treating text as if upper and lower case characters of the same letter are different.
 See also: [case-insensitive](#case-insensitive).
 
-comment
+[comment]{#comment}
 :   A remark in a program that is intended to help human readers understand what is going on,
 but is ignored by the computer.
 Comments in Python, R, and the Unix shell start with a `#` character and
@@ -48,60 +48,60 @@ run to the end of the line;
 comments in SQL start with `--`,
 and other languages have other conventions.
 
-compose
+[compose]{#compose}
 :   To apply one function to the result of another, such as `f(g(x))`.
 
-conditional statement
+[conditional statement]{#conditional-statement}
 :   A statement in a program that might or might not be executed
 depending on whether a test is true or false.
 
-comma-separated values
+[comma-separated values]{#comma-separated-values}
 :   (CSV) A common textual representation for tables
 in which the values in each row are separated by commas.
 
-default value
+[default value]{#default-value}
 :   A value to use for a [parameter](#parameter) if nothing is specified explicitly.
 
-defensive programming
+[defensive programming]{#defensive-programming}
 :   The practice of writing programs that check their own operation
 to catch errors as early as possible.
 
-delimiter
+[delimiter]{#delimiter}
 :   A character or characters used to separate individual values,
 such as the commas between columns in a [CSV](#comma-separated-values) file.
 
-docstring
+[docstring]{#docstring}
 :   Short for "documentation string",
 this refers to textual documentation embedded in Python programs.
 Unlike comments, docstrings are preserved in the running program
 and can be examined in interactive sessions.
 
-documentation
+[documentation]{#documentation}
 :   Human-language text written to explain what software does,
 how it works, or how to use it.
 
-dotted notation
+[dotted notation]{#dotted-notation}
 :   A two-part notation used in many programming languages
 in which `thing.component` refers to the `component` belonging to `thing`.
 
-empty string
+[empty string]{#empty-string}
 :   A character string containing no characters,
 often thought of as the "zero" of text.
 
-encapsulation
+[encapsulation]{#encapsulation}
 :   The practice of hiding something's implementation details
 so that the rest of a program can worry about *what* it does
 rather than *how* it does it.
 
-floating-point number
+[floating-point number]{#floating-point-number}
 :   A number containing a fractional part and an exponent.
 See also: [integer](#integer).
 
-for loop
+[for loop]{#for-loop}
 :   A loop that is executed once for each value in some kind of set, list, or range.
 See also: [while loop](#while-loop).
 
-function
+[function]{#function}
 :   A named group of instructions that is executed when the function's name is used in
 the code. Occurrence of a function name in the code is a [function call](#function-call).
 Functions may process input [arguments](#argument) and return the result back. Functions
@@ -110,191 +110,191 @@ need to return any meaningful value and can be written without the
 [`return` statement](#return-statement) completely.
 Such functions return a special value `None`, which is a way of saying "nothing" in Python.
 
-function call
+[function call]{#function-call}
 :   A use of a function in another piece of software.
 
-global variable
+[global variable]{#global-variable}
 :   A variable defined outside of a function. It can be used in global statements,
 and read inside functions.
 
-heat map
+[heat map]{#heat-map}
 :   A graphical representation of two-dimensional data in which colors,
 ranging on a scale of hue or intensity, represent the data values.
 
-immutable
+[immutable]{#immutable}
 :   Unchangeable.
 The value of immutable data cannot be altered after it has been created.
 See also: [mutable](#mutable).
 
-import
+[import]{#import}
 :   To load a [library](#library) into a program.
 
-in-place operators
+[in-place operators]{#in-place-operators}
 :   An operator such as `+=` that provides a shorthand notation for
 the common case in which the variable being assigned to
 is also an operand on the right hand side of the assignment.
 For example, the statement `x += 3` means the same thing as `x = x + 3`.
 
-index
+[index]{#index}
 :   A subscript that specifies the location of a single value in a collection,
 such as a single pixel in an image.
 
-inner loop
+[inner loop]{#inner-loop}
 :   A loop that is inside another loop. See also: [outer loop](#outer-loop).
 
-integer
+[integer]{#integer}
 :   A whole number, such as -12343. See also: [floating-point number](#floating-point-number).
 
-invariant
+[invariant]{#invariant}
 :   An expression whose value doesn't change during the execution of a program,
 typically used in an [assertion](#assertion).
 See also: [precondition](#precondition), [postcondition](#postcondition).
 
-library
+[library]{#library}
 :   A family of code units (functions, classes, variables) that implement a set of
 related tasks.
 
-local variable
+[local variable]{#local-variable}
 :   A variable defined inside of a function, that exists only in the scope of that
 function, meaning it cannot be accessed by code outside of the function.
 
-loop variable
+[loop variable]{#loop-variable}
 :   The variable that keeps track of the progress of the loop.
 
-member
+[member]{#member}
 :   A variable contained within an [object](#object).
 
-method
+[method]{#method}
 :   A function which is tied to a particular [object](#object).
 Each of an object's methods typically implements one of the things it can do,
 or one of the questions it can answer.
 
-mutable
+[mutable]{#mutable}
 :   Changeable. The value of mutable data can be altered after it has been
 created. See [immutable](#immutable)."
 
-notebook
+[notebook]{#notebook}
 :   Interactive computational environment accessed via your web browser, in which you can write
 and execute Python code and combine it with explanatory text, mathematics and visualizations.
 Examples are IPython or Jupyter notebooks.
 
-object
+[object]{#object}
 :   A collection of conceptually related variables ([members](#member)) and
 functions using those variables ([methods](#method)).
 
-outer loop
+[outer loop]{#outer-loop}
 :   A loop that contains another loop.
 See also: [inner loop](#inner-loop).
 
-parameter
+[parameter]{#parameter}
 :   A variable named in the function's declaration that is used to
 hold a value passed into the call.
 The term is often used interchangeably (and inconsistently) with [argument](#argument).
 
-pipe
+[pipe]{#pipe}
 :   A connection from the output of one program to the input of another.
 When two or more programs are connected in this way, they are called a "pipeline".
 
-postcondition
+[postcondition]{#postcondition}
 :   A condition that a function (or other block of code) guarantees is true
 once it has finished running.
 Postconditions are often represented using [assertions](#assertion).
 
-precondition
+[precondition]{#precondition}
 :   A condition that must be true in order for a function (or other block of code)
 to run correctly.
 
-regression
+[regression]{#regression}
 :   To re-introduce a bug that was once fixed.
 
-return statement
+[return statement]{#return-statement}
 :   A statement that causes a function to stop executing and return a value
 to its caller immediately.
 
-RGB
+[RGB]{#rgb}
 :   An [additive model](#additive-color-model)
 that represents colors as combinations of red, green, and blue.
 Each color's value is typically in the range 0..255
 (i.e., a one-byte integer).
 
-sequence
+[sequence]{#sequence}
 :   A collection of information that is presented in a specific order.
 For example, in Python, a [string](#string) is a sequence of characters,
 while a list is a sequence of any variable.
 
-shape
+[shape]{#shape}
 :   An array's dimensions, represented as a vector.
 For example, a 5×3 array's shape is `(5,3)`.
 
-silent failure
+[silent failure]{#silent-failure}
 :   Failing without producing any warning messages.
 Silent failures are hard to detect and debug.
 
-slice
+[slice]{#slice}
 :   A regular subsequence of a larger sequence,
 such as the first five elements or every second element.
 
-stack frame
+[stack frame]{#stack-frame}
 :   A data structure that provides storage for a function's local variables.
 Each time a function is called, a new stack frame is created
 and put on the top of the [call stack](#call-stack). When the function returns,
 the stack frame is discarded.
 
-standard input
+[standard input]{#standard-input}
 :   A process's default input stream.
 In interactive command-line applications,
 it is typically connected to the keyboard; in a [pipe](#pipe),
 it receives data from the [standard output](#standard-output) of the preceding process.
 
-standard output
+[standard output]{#standard-output}
 :   A process's default output stream.
 In interactive command-line applications,
 data sent to standard output is displayed on the screen;
 in a [pipe](#pipe),
 it is passed to the [standard input](#standard-input) of the next process.
 
-string
+[string]{#string}
 :   Short for "character string",
 a [sequence](#sequence) of zero or more characters.
 
-syntax
+[syntax]{#syntax}
 :   The rules that define how code must be written for a computer to understand.
 
-syntax error
+[syntax error]{#syntax-error}
 :   A programming error that occurs when statements are in an order or contain characters
 not expected by the programming language.
 
-tab completion
+[tab completion]{#tab-completion}
 :   A feature of command-line interpreters, in which the program automatically fills in partially
 typed commands upon pressing the <kbd>Tab</kbd> key.
 
-test oracle
+[test oracle]{#test-oracle}
 :   A program, device, data set, or human being
 against which the results of a test can be compared.
 
-test-driven development
+[test-driven development]{#test-driven-development}
 :   The practice of writing unit tests *before* writing the code they test.
 
-traceback
+[traceback]{#traceback}
 :   The sequence of function calls that led to an error.
 
-tuple
+[tuple]{#tuple}
 :   An [immutable](#immutable) [sequence](#sequence) of values.
 
-type
+[type]{#type}
 :   The classification of something in a program (for example, the contents of a variable)
 as a kind of number (e.g. [floating-point](#float), [integer](#integer)),
 [string](#string), or something else.
 
-type of error
+[type of error]{#type-of-error}
 :   Indicates the nature of an error in a program. For example, in Python,
 an `IOError` to problems with file input/output.
 See also: [syntax error](#syntax-error).
 
-variable
+[variable]{#variable}
 :   A value that has a name associated with it.
 
-while loop
+[while loop]{#while-loop}
 :   A loop that keeps executing as long as some condition is true.
 See also: [for loop](#for-loop).
 
diff --git a/learners/setup.md b/learners/setup.md
index 3958c7057..aa72a89d6 100644
--- a/learners/setup.md
+++ b/learners/setup.md
@@ -41,6 +41,12 @@ you like.
 A Jupyter Notebook provides a browser-based interface for working with Python.
 If you installed Anaconda, you can launch a notebook in two ways:
 
+:::::::::::::::::::::::::::::::::::::::: {.empty-div style="margin-bottom: 50px"}
+
+<!-- This div is intentionally empty to allow the solution to float alone-->
+
+::::::::::::::::::::::::::::::::::::::::
+
 :::::::::::::::  solution
 
 ## Anaconda Navigator
@@ -58,16 +64,27 @@ If you installed Anaconda, you can launch a notebook in two ways:
   ![](fig/jupyter-notebook-data-directory.png){alt='Anaconda Navigator Notebook directory'}
 4. Launch the notebook by clicking on the "New" button and then selecting "Python 3":
   ![](fig/jupyter-notebook-launch-notebook.png){alt='Anaconda Navigator Notebook directory'}
-  
 
 :::::::::::::::::::::::::
 
+:::::::::::::::::::::::::::::::::::::::: {.empty-div style="margin-bottom: 50px"}
+
+<!-- This div is intentionally empty to allow the solution to float alone-->
+
+::::::::::::::::::::::::::::::::::::::::
+
 :::::::::::::::  solution
 
 ## Command line (Terminal)
 
 1\. Navigate to the `data` directory:
 
+:::::::::::::::::::::::::::::::::::::::: {.empty-div style="margin-bottom: 50px"}
+
+<!-- This div is intentionally empty to allow the solution to float alone-->
+
+::::::::::::::::::::::::::::::::::::::::
+
 :::::::::::::::  solution
 
 ## Unix shell
@@ -81,6 +98,12 @@ cd ~/Desktop/swc-python/data
 
 :::::::::::::::::::::::::
 
+:::::::::::::::::::::::::::::::::::::::: {.empty-div style="margin-bottom: 50px"}
+
+<!-- This div is intentionally empty to allow the solution to float alone-->
+
+::::::::::::::::::::::::::::::::::::::::
+
 :::::::::::::::  solution
 
 ## Command Prompt (Windows)
@@ -98,6 +121,12 @@ cd /D %userprofile%\Desktop\swc-python\data
 
 2\. Start Jupyter server
 
+:::::::::::::::::::::::::::::::::::::::: {.empty-div style="margin-bottom: 50px"}
+
+<!-- This div is intentionally empty to allow the solution to float alone-->
+
+::::::::::::::::::::::::::::::::::::::::
+
 :::::::::::::::  solution
 
 ## Unix shell
@@ -108,6 +137,12 @@ jupyter notebook
 
 :::::::::::::::::::::::::
 
+:::::::::::::::::::::::::::::::::::::::: {.empty-div style="margin-bottom: 50px"}
+
+<!-- This div is intentionally empty to allow the solution to float alone-->
+
+::::::::::::::::::::::::::::::::::::::::
+
 :::::::::::::::  solution
 
 ## Command Prompt (Windows)
@@ -122,7 +157,6 @@ python -m notebook
 from the drop-down menu:
 ![](fig/jupyter-notebook-launch-notebook2.png){alt='Anaconda Navigator Notebook directory'}
 
-
 :::::::::::::::::::::::::
 
   <!-- vertical spacer -->
@@ -160,7 +194,7 @@ winpty python
 [anaconda-instructions]: https://carpentries.github.io/workshop-template/#python
 [anaconda-install]: https://docs.anaconda.com/anaconda/install
 [zipfile1]: data/python-novice-inflammation-data.zip
-[zipfile2]: code/python-novice-inflammation-code.zip
+[zipfile2]: ../episodes/files/code/python-novice-inflammation-code.zip
 [gitbash]: https://gitforwindows.org