diff --git a/book-example/src/format/config.md b/book-example/src/format/config.md
index 3100b930..d1980a21 100644
--- a/book-example/src/format/config.md
+++ b/book-example/src/format/config.md
@@ -11,10 +11,10 @@ author = "John Doe"
 description = "The example book covers examples."
 
 [build]
+build-dir = "my-example-book"
 create-missing = false
 
 [output.html]
-destination = "my-example-book"
 additional-css = ["custom.css"]
 ```
 
@@ -35,8 +35,6 @@ This is general information about your book.
 - **src:** By default, the source directory is found in the directory named
   `src` directly under the root folder. But this is configurable with the `src`
   key in the configuration file.
-- **build-dir:** The directory to put the rendered book in. By default this is
-  `book/` in the book's root directory.
 
 **book.toml**
 ```toml
@@ -45,20 +43,23 @@ title = "Example book"
 authors = ["John Doe", "Jane Doe"]
 description = "The example book covers examples."
 src = "my-src"  # the source files will be found in `root/my-src` instead of `root/src`
-build-dir = "build"
 ```
 
 ### Build options
 
 This controls the build process of your book.
 
+- **build-dir:** The directory to put the rendered book in. By default this is
+  `book/` in the book's root directory.
 - **create-missing:** By default, any missing files specified in `SUMMARY.md`
-  will be created when the book is built. If this is `false` then the build
-  process will instead exit with an error if any files do not exist.
+  will be created when the book is built (i.e. `create-missing = true`). If this
+  is `false` then the build process will instead exit with an error if any files
+  do not exist.
 
 **book.toml**
 ```toml
 [build]
+build-dir = "build"
 create-missing = false
 ```
 
diff --git a/src/bin/build.rs b/src/bin/build.rs
index a7278c66..54dffbd1 100644
--- a/src/bin/build.rs
+++ b/src/bin/build.rs
@@ -28,11 +28,12 @@ pub fn execute(args: &ArgMatches) -> Result<()> {
     let mut book = MDBook::new(&book_dir).read_config()?;
 
     if let Some(dest_dir) = args.value_of("dest-dir") {
-        book.config.book.build_dir = PathBuf::from(dest_dir);
+        book.config.build.build_dir = PathBuf::from(dest_dir);
     }
 
+    // This flag is deprecated in favor of being set via `book.toml`.
     if args.is_present("no-create") {
-        book.create_missing = Some(false);
+        book.config.build.create_missing = false;
     }
 
     book.build()?;
diff --git a/src/bin/serve.rs b/src/bin/serve.rs
index 87099411..ac1ba144 100644
--- a/src/bin/serve.rs
+++ b/src/bin/serve.rs
@@ -52,7 +52,7 @@ pub fn execute(args: &ArgMatches) -> Result<()> {
     let mut book = MDBook::new(&book_dir).read_config()?;
 
     if let Some(dest_dir) = args.value_of("dest-dir") {
-        book.config.book.build_dir = PathBuf::from(dest_dir);
+        book.config.build.build_dir = PathBuf::from(dest_dir);
     }
 
     let port = args.value_of("port").unwrap_or("3000");
diff --git a/src/bin/watch.rs b/src/bin/watch.rs
index 39862d18..29772715 100644
--- a/src/bin/watch.rs
+++ b/src/bin/watch.rs
@@ -30,7 +30,7 @@ pub fn execute(args: &ArgMatches) -> Result<()> {
     let mut book = MDBook::new(&book_dir).read_config()?;
 
     if let Some(dest_dir) = args.value_of("dest-dir") {
-        book.config.book.build_dir = PathBuf::from(dest_dir);
+        book.config.build.build_dir = PathBuf::from(dest_dir);
     }
 
     if args.is_present("open") {
diff --git a/src/book/mod.rs b/src/book/mod.rs
index a412bc55..ada24fe1 100644
--- a/src/book/mod.rs
+++ b/src/book/mod.rs
@@ -23,12 +23,6 @@ pub struct MDBook {
     renderer: Box<Renderer>,
 
     pub livereload: Option<String>,
-
-    /// Should `mdbook build` create files referenced from SUMMARY.md if they
-    /// don't exist? If `None`, use the setting specified in `book.toml`,
-    /// otherwise use this.
-    /// This is for backward compatibility only.
-    pub create_missing: Option<bool>,
 }
 
 impl MDBook {
@@ -73,7 +67,6 @@ impl MDBook {
             renderer: Box::new(HtmlHandlebars::new()),
 
             livereload: None,
-            create_missing: None,
         }
     }
 
@@ -181,9 +174,7 @@ impl MDBook {
                 let path = self.get_source().join(&ch.path);
 
                 if !path.exists() {
-                    let create_missing = self.create_missing.unwrap_or(self.config.build.create_missing);
-
-                    if !create_missing {
+                    if !self.config.build.create_missing {
                         return Err(
                             format!("'{}' referenced from SUMMARY.md does not exist.", path.to_string_lossy()).into(),
                         );
@@ -388,7 +379,7 @@ impl MDBook {
     }
 
     pub fn get_destination(&self) -> PathBuf {
-        self.root.join(&self.config.book.build_dir)
+        self.root.join(&self.config.build.build_dir)
     }
 
     pub fn get_source(&self) -> PathBuf {
diff --git a/src/config.rs b/src/config.rs
index dac67b66..d23e7a80 100644
--- a/src/config.rs
+++ b/src/config.rs
@@ -92,7 +92,7 @@ impl Config {
         get_and_insert!(table, "description" => cfg.book.description);
 
         // This complicated chain of and_then's is so we can move 
-        // "output.html.destination" to "book.build_dir" and parse it into a 
+        // "output.html.destination" to "build.build_dir" and parse it into a 
         // PathBuf.
         let destination: Option<PathBuf> = table.get_mut("output")
             .and_then(|output| output.as_table_mut())
@@ -102,7 +102,7 @@ impl Config {
             .and_then(|dest| dest.try_into().ok());
 
         if let Some(dest) = destination {
-            cfg.book.build_dir = dest;
+            cfg.build.build_dir = dest;
         }
 
         cfg.rest = table;
@@ -163,8 +163,10 @@ impl<'de> Deserialize<'de> for Config {
             warn!("It looks like you are using the legacy book.toml format.");
             warn!("We'll parse it for now, but you should probably convert to the new format.");
             warn!("See the mdbook documentation for more details, although as a rule of thumb");
-            warn!("just move all top level configuration entries like `title`, `author` and ");
-            warn!("`description` under a table called `[book]` and it should all work.");
+            warn!("just move all top level configuration entries like `title`, `author` and");
+            warn!("`description` under a table called `[book]`, move the `destination` entry");
+            warn!("from `[output.html]`, renamed to `build-dir`, under a table called");
+            warn!("`[build]`, and it should all work.");
             warn!("Documentation: http://rust-lang-nursery.github.io/mdBook/format/config.html");
             return Ok(Config::from_legacy(table));
         }
@@ -205,8 +207,6 @@ pub struct BookConfig {
     pub description: Option<String>,
     /// Location of the book source relative to the book's root directory.
     pub src: PathBuf,
-    /// Where to put built artefacts relative to the book's root directory.
-    pub build_dir: PathBuf,
     /// Does this book support more than one language?
     pub multilingual: bool,
 }
@@ -218,7 +218,6 @@ impl Default for BookConfig {
             authors: Vec::new(),
             description: None,
             src: PathBuf::from("src"),
-            build_dir: PathBuf::from("book"),
             multilingual: false,
         }
     }
@@ -228,6 +227,8 @@ impl Default for BookConfig {
 #[derive(Debug, Clone, PartialEq, Serialize, Deserialize)]
 #[serde(default, rename_all = "kebab-case")]
 pub struct BuildConfig {
+    /// Where to put built artefacts relative to the book's root directory.
+    pub build_dir: PathBuf,
     /// Should non-existent markdown files specified in `SETTINGS.md` be created
     /// if they don't exist?
     pub create_missing: bool,
@@ -236,6 +237,7 @@ pub struct BuildConfig {
 impl Default for BuildConfig {
     fn default() -> BuildConfig {
         BuildConfig {
+            build_dir: PathBuf::from("book"),
             create_missing: true,
         }
     }
@@ -272,9 +274,9 @@ mod tests {
         description = "A completely useless book"
         multilingual = true
         src = "source"
-        build-dir = "outputs"
 
         [build]
+        build-dir = "outputs"
         create-missing = false
 
         [output.html]
@@ -298,10 +300,10 @@ mod tests {
             description: Some(String::from("A completely useless book")),
             multilingual: true,
             src: PathBuf::from("source"),
-            build_dir: PathBuf::from("outputs"),
             ..Default::default()
         };
         let build_should_be = BuildConfig {
+            build_dir: PathBuf::from("outputs"),
             create_missing: false,
         };
         let playpen_should_be = Playpen {
@@ -397,11 +399,15 @@ mod tests {
                 "Create book from markdown files. Like Gitbook but implemented in Rust",
             )),
             authors: vec![String::from("Mathieu David")],
-            build_dir: PathBuf::from("my-book"),
             src: PathBuf::from("./source"),
             ..Default::default()
         };
 
+        let build_should_be = BuildConfig {
+            build_dir: PathBuf::from("my-book"),
+            create_missing: true,
+        };
+
         let html_should_be = HtmlConfig {
             theme: Some(PathBuf::from("my-theme")),
             curly_quotes: true,
@@ -413,6 +419,7 @@ mod tests {
 
         let got = Config::from_str(src).unwrap();
         assert_eq!(got.book, book_should_be);
+        assert_eq!(got.build, build_should_be);
         assert_eq!(got.html_config().unwrap(), html_should_be);
     }
 }
diff --git a/src/lib.rs b/src/lib.rs
index 2cf5e3e7..3991ae95 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -28,7 +28,7 @@
 //!     
 //!     // tweak the book configuration a bit
 //!     md.config.book.src = PathBuf::from("source");
-//!     md.config.book.build_dir = PathBuf::from("book");
+//!     md.config.build.build_dir = PathBuf::from("book");
 //! 
 //!     // Render the book
 //!     md.build().unwrap();                        
diff --git a/tests/init.rs b/tests/init.rs
index 0dff7db3..e35edee6 100644
--- a/tests/init.rs
+++ b/tests/init.rs
@@ -42,7 +42,7 @@ fn run_mdbook_init_with_custom_book_and_src_locations() {
 
     let mut md = MDBook::new(temp.path());
     md.config.book.src = PathBuf::from("in");
-    md.config.book.build_dir = PathBuf::from("out");
+    md.config.build.build_dir = PathBuf::from("out");
 
     md.init().unwrap();