diff --git a/manual/src/SUMMARY.md b/manual/src/SUMMARY.md
index abeb6c271c4e8c47ba20f95f5506a1ed5a0b4650..4aea60b94f9772f60e352de34c09d24eeba24e32 100644
--- a/manual/src/SUMMARY.md
+++ b/manual/src/SUMMARY.md
@@ -11,7 +11,8 @@
     - [Quoting Rules](ch03-03-quotation.md)
     - [Multi-line Arguments](ch03-04-multiargs.md)
     - [Multi-line Comments](ch03-05-multicomments.md)
-    - [General Tips](ch03-06-general.md)
+    - [Prompt Function](ch03-06-prompt_fn.md)
+    - [General Tips](ch03-07-general.md)
 
 - [Variable Assignments](ch04-00-variables.md)
 
diff --git a/manual/src/ch02-00-features.md b/manual/src/ch02-00-features.md
index d8733c7198c9c8502adf1699a31a580dd09899b1..ead022319c1bd5175500203edf728e3fae95177b 100644
--- a/manual/src/ch02-00-features.md
+++ b/manual/src/ch02-00-features.md
@@ -1,46 +1 @@
 # Features
-
-## Miscellaneous Features
-
-Small features that don't belong in any specific category.
-
-[Miscellaneous Features](ch03-00-miscellaneous.html)
-
-
-## Shell Expansions / Substitutions
-
-Expansions provide dynamic string generation capabilities. These work identical to the standard
-POSIX way, but there are a few major differences: arrays are denoted with an **@** sigil, and have
-their own variant of process expansions (**@()**) which splits outputs by whitespace; the
-arithmetic logic is more feature-complete, supports floating-point math, and handles larger
-numbers; and Ion supports methods in the same manner as the [Oil shell](http://www.oilshell.org/).
-
-[Expansions](ch05-00-expansions.html)
-- [Variable Expansions](ch05-01-variable.html)
-- [Process Expansions](ch05-02-process.html)
-- [Brace Expansions](ch05-03-brace.html)
-- [Arithmetic Expansions](ch05-04-arithmetic.html)
-- [Method Expansions](ch05-05-method.html)
-
-## Slicing Syntax
-
-A critical feature over POSIX shells, Ion provides the ability to slice expansions with a familiar
-syntax. The supplied index or range is expanded, and then handled according to whether the
-expanded value is an index, inclusive range, or exclusive range. This eliminates much of the need
-for temporarily storing and/or piping values to other commands, instead performing the slicing at
-parse-time.
-
-[Slicing Syntax](ch06-00-slicing.html)
-
-## Control Flow
-
-As Ion features an imperative paradigm, the order that statements are evaluated and executed is
-determined by various control flow keywords, such as `if`, `while`, `for`, `break`, and
-`continue`. Ion's control flow logic is very similar to POSIX shells, but there are a few major
-differences, such as that all blocks are ended with the `end` keyword; and the `do`/`then`
-keywords aren't necessary.
-
-[Control Flow](ch07-00-flow.html)
-- [Conditionals](ch07-01-conditionals.html)
-- [Loops](ch07-02-loops.html)
-- [Matches](ch07-03-matches.html)
diff --git a/manual/src/ch03-00-miscellaneous.md b/manual/src/ch03-00-miscellaneous.md
index 3be26a92fb37a6cea6c22245454178075414accf..bc67b1ddffb8ab06d1f204973a529ae99cbeb056 100644
--- a/manual/src/ch03-00-miscellaneous.md
+++ b/manual/src/ch03-00-miscellaneous.md
@@ -1,11 +1,3 @@
 # Miscellaneous Features
 
 These are features of Ion that don't belong to any specific category:
-
-- [Implicit `cd`](ch03-01-implicitcd.html)
-- [XDG App Directories](ch03-02-xdg.html)
-- [Quoting Rules](ch03-03-quotation.html)
-- [Multi-line Arguments](ch03-04-multiargs.html)
-- [Multi-line Comments](ch03-05-multicomments.html)
-- [General Tips](ch03-06-general.html)
-- [Prompt Function](ch03-07-prompt_fn.html)
diff --git a/manual/src/ch03-07-prompt_fn.md b/manual/src/ch03-06-prompt_fn.md
similarity index 100%
rename from manual/src/ch03-07-prompt_fn.md
rename to manual/src/ch03-06-prompt_fn.md
diff --git a/manual/src/ch03-06-general.md b/manual/src/ch03-07-general.md
similarity index 100%
rename from manual/src/ch03-06-general.md
rename to manual/src/ch03-07-general.md
diff --git a/manual/src/ch05-00-expansions.md b/manual/src/ch05-00-expansions.md
index 9f9d0cdf611f331e6e07c151a5d4b30517c38279..f9e344f90cc32739944da8bd76d7502f1ce4b3d9 100644
--- a/manual/src/ch05-00-expansions.md
+++ b/manual/src/ch05-00-expansions.md
@@ -5,9 +5,3 @@ POSIX way, but there are a few major differences: arrays are denoted with an **@
 their own variant of process expansions (**@()**) which splits outputs by whitespace; the
 arithmetic logic is more feature-complete, supports floating-point math, and handles larger
 numbers; and Ion supports methods in the same manner as the [Oil shell](http://www.oilshell.org/).
-
-- [Variable Expansions](ch05-01-variable.html)
-- [Process Expansions](ch05-02-process.html)
-- [Brace Expansions](ch05-03-brace.html)
-- [Arithmetic Expansions](ch05-04-arithmetic.html)
-- [Method Expansions](ch05-05-method.html)
diff --git a/manual/src/ch07-00-flow.md b/manual/src/ch07-00-flow.md
index c4fec6d6995b25dd09efe3cb3fc2dcdca85a59e9..c755749c9045962e42e60bc9ba4b3f365a356403 100644
--- a/manual/src/ch07-00-flow.md
+++ b/manual/src/ch07-00-flow.md
@@ -5,7 +5,3 @@ determined by various control flow keywords, such as `if`, `while`, `for`, `brea
 `continue`. Ion's control flow logic is very similar to POSIX shells, but there are a few major
 differences, such as that all blocks are ended with the `end` keyword; and the `do`/`then`
 keywords aren't necessary.
-
-- [Conditionals](ch07-01-conditionals.html)
-- [Loops](ch07-02-loops.html)
-- [Matches](ch07-03-matches.html)
diff --git a/manual/src/ch08-functions.md b/manual/src/ch08-00-functions.md
similarity index 93%
rename from manual/src/ch08-functions.md
rename to manual/src/ch08-00-functions.md
index dd8f762452671ec6b0a7f9b28275830f609f7c9a..20b915e0ed567d6a9c722acaf64ad21b9167bcc9 100644
--- a/manual/src/ch08-functions.md
+++ b/manual/src/ch08-00-functions.md
@@ -46,7 +46,7 @@ You'd get as output of that script:
 ion: function argument has invalid type: expected int, found value 'a'
 ```
 
-You can use any of the [supported types](ch04-00-variables.html#Supported Types).
+You can use any of the [supported types](ch04-00-variables.md#Supported Types).
 
 ## Function piping
 
diff --git a/manual/src/ch13-00-examples.md b/manual/src/ch13-00-examples.md
deleted file mode 100644
index 3a6ae7af03b5faaa8a67f7edde7242ae019e7242..0000000000000000000000000000000000000000
--- a/manual/src/ch13-00-examples.md
+++ /dev/null
@@ -1 +0,0 @@
-# Ion by Example
diff --git a/manual/src/ch14-00-history.md b/manual/src/ch13-00-history.md
similarity index 100%
rename from manual/src/ch14-00-history.md
rename to manual/src/ch13-00-history.md