13 files changed, 239 insertions, 29 deletions
diff --git a/doc/default.nix b/doc/default.nix
index ec458634a42..1adcd796820 100644
--- a/doc/default.nix
+++ b/doc/default.nix
@@ -45,45 +45,45 @@ pkgs.stdenv.mkDerivation {
     cp -s '${sources-langs}'/* ./languages-frameworks
   ''
   + toDocbook {
-      inputFile = ./introduction.md;
-      outputFile = "introduction.xml";
+      inputFile = ./introduction.chapter.md;
+      outputFile = "introduction.chapter.xml";
       useChapters = true;
     }
   + toDocbook {
-      inputFile = ./shell.md;
-      outputFile = "shell.xml";
+      inputFile = ./shell.section.md;
+      outputFile = "shell.section.xml";
     }
   + toDocbook {
-      inputFile = ./languages-frameworks/python.md;
-      outputFile = "./languages-frameworks/python.xml";
+      inputFile = ./languages-frameworks/python.section.md;
+      outputFile = "./languages-frameworks/python.section.xml";
     }
   + toDocbook {
-      inputFile = ./languages-frameworks/haskell.md;
-      outputFile = "./languages-frameworks/haskell.xml";
+      inputFile = ./languages-frameworks/haskell.section.md;
+      outputFile = "./languages-frameworks/haskell.section.xml";
     }
   + toDocbook {
-      inputFile = ../pkgs/development/idris-modules/README.md;
-      outputFile = "languages-frameworks/idris.xml";
+      inputFile = ./languages-frameworks/idris.section.md;
+      outputFile = "languages-frameworks/idris.section.xml";
     }
   + toDocbook {
-      inputFile = ../pkgs/development/node-packages/README.md;
-      outputFile = "languages-frameworks/node.xml";
+      inputFile = ./languages-frameworks/node.section.md;
+      outputFile = "languages-frameworks/node.section.xml";
     }
   + toDocbook {
-      inputFile = ../pkgs/development/r-modules/README.md;
-      outputFile = "languages-frameworks/r.xml";
+      inputFile = ./languages-frameworks/r.section.md;
+      outputFile = "languages-frameworks/r.section.xml";
     }
   + toDocbook {
-      inputFile = ./languages-frameworks/rust.md;
-      outputFile = "./languages-frameworks/rust.xml";
+      inputFile = ./languages-frameworks/rust.section.md;
+      outputFile = "./languages-frameworks/rust.section.xml";
     }
   + toDocbook {
-      inputFile = ./languages-frameworks/vim.md;
-      outputFile = "./languages-frameworks/vim.xml";
+      inputFile = ./languages-frameworks/vim.section.md;
+      outputFile = "./languages-frameworks/vim.section.xml";
     }
   + toDocbook {
-      inputFile = ./languages-frameworks/emscripten.md;
-      outputFile = "./languages-frameworks/emscripten.xml";
+      inputFile = ./languages-frameworks/emscripten.section.md;
+      outputFile = "./languages-frameworks/emscripten.section.xml";
     }
   + ''
     echo ${lib.nixpkgsVersion} > .version
diff --git a/doc/introduction.md b/doc/introduction.chapter.md
index 8b03221c64b..8b03221c64b 100644
--- a/doc/introduction.md
+++ b/doc/introduction.chapter.md
diff --git a/doc/languages-frameworks/emscripten.md b/doc/languages-frameworks/emscripten.section.md
index 24c49ec1409..24c49ec1409 100644
--- a/doc/languages-frameworks/emscripten.md
+++ b/doc/languages-frameworks/emscripten.section.md
diff --git a/doc/languages-frameworks/haskell.md b/doc/languages-frameworks/haskell.section.md
index 1623e0d276f..1623e0d276f 100644
--- a/doc/languages-frameworks/haskell.md
+++ b/doc/languages-frameworks/haskell.section.md
diff --git a/doc/languages-frameworks/idris.section.md b/doc/languages-frameworks/idris.section.md
new file mode 100644
index 00000000000..005ed360285
--- /dev/null
+++ b/doc/languages-frameworks/idris.section.md
@@ -0,0 +1,39 @@
+Idris packages
+==============
+
+This directory contains build rules for idris packages. In addition,
+it contains several functions to build and compose those packages.
+Everything is exposed to the user via the `idrisPackages` attribute.
+
+callPackage
+------------
+
+This is like the normal nixpkgs callPackage function, specialized to
+idris packages.
+
+builtins
+---------
+
+This is a list of all of the libraries that come packaged with Idris
+itself.
+
+build-idris-package
+--------------------
+
+A function to build an idris package. Its sole argument is a set like
+you might pass to `stdenv.mkDerivation`, except `build-idris-package`
+sets several attributes for you. See `build-idris-package.nix` for
+details.
+
+build-builtin-package
+----------------------
+
+A version of `build-idris-package` specialized to builtin libraries.
+Mostly for internal use.
+
+with-packages
+-------------
+
+Bundle idris together with a list of packages. Because idris currently
+only supports a single directory in its library path, you must include
+all desired libraries here, including `prelude` and `base`.
\ No newline at end of file
diff --git a/doc/languages-frameworks/index.xml b/doc/languages-frameworks/index.xml
index 6743c131201..a1c265f6748 100644
--- a/doc/languages-frameworks/index.xml
+++ b/doc/languages-frameworks/index.xml
@@ -17,20 +17,20 @@ such as Perl or Haskell.  These are described in this chapter.</para>
 <xi:include href="bower.xml" />
 <xi:include href="coq.xml" />
 <xi:include href="go.xml" />
-<xi:include href="haskell.xml" />
-<xi:include href="idris.xml" /> <!-- generated from ../../pkgs/development/idris-modules/README.md  -->
+<xi:include href="haskell.section.xml" />
+<xi:include href="idris.section.xml" />
 <xi:include href="java.xml" />
 <xi:include href="lua.xml" />
-<xi:include href="node.xml" /> <!-- generated from ../../pkgs/development/node-packages/README.md  -->
+<xi:include href="node.section.xml" />
 <xi:include href="perl.xml" />
-<xi:include href="python.xml" />
+<xi:include href="python.section.xml" />
 <xi:include href="qt.xml" />
-<xi:include href="r.xml" /> <!-- generated from ../../pkgs/development/r-modules/README.md  -->
+<xi:include href="r.section.xml" />
 <xi:include href="ruby.xml" />
-<xi:include href="rust.xml" />
+<xi:include href="rust.section.xml" />
 <xi:include href="texlive.xml" />
-<xi:include href="vim.xml" />
-<xi:include href="emscripten.xml" />
+<xi:include href="vim.section.xml" />
+<xi:include href="emscripten.section.xml" />
 
 
 </chapter>
diff --git a/doc/languages-frameworks/node.section.md b/doc/languages-frameworks/node.section.md
new file mode 100644
index 00000000000..17a203ed12b
--- /dev/null
+++ b/doc/languages-frameworks/node.section.md
@@ -0,0 +1,51 @@
+Node.js packages
+================
+The `pkgs/development/node-packages` folder contains a generated collection of
+[NPM packages](https://npmjs.com/) that can be installed with the Nix package
+manager.
+
+As a rule of thumb, the package set should only provide *end user* software
+packages, such as command-line utilities. Libraries should only be added to the
+package set if there is a non-NPM package that requires it.
+
+When it is desired to use NPM libraries in a development project, use the
+`node2nix` generator directly on the `package.json` configuration file of the
+project.
+
+The package set also provides support for multiple Node.js versions. The policy
+is that a new package should be added to the collection for the latest stable LTS
+release (which is currently 6.x), unless there is an explicit reason to support
+a different release.
+
+If your package uses native addons, you need to examine what kind of native
+build system it uses. Here are some examples:
+
+* `node-gyp`
+* `node-gyp-builder`
+* `node-pre-gyp`
+
+After you have identified the correct system, you need to override your package
+expression while adding in build system as a build input. For example, `dat`
+requires `node-gyp-build`, so we override its expression in `default-v6.nix`:
+
+```nix
+dat = nodePackages.dat.override (oldAttrs: {
+  buildInputs = oldAttrs.buildInputs ++ [ nodePackages.node-gyp-build ];
+});
+```
+
+To add a package from NPM to nixpkgs:
+
+ 1. Modify `pkgs/development/node-packages/node-packages-v6.json` to add, update
+    or remove package entries. (Or `pkgs/development/node-packages/node-packages-v4.json`
+    for packages depending on Node.js 4.x)
+ 2. Run the script: `(cd pkgs/development/node-packages && ./generate.sh)`.
+ 3. Build your new package to test your changes:
+    `cd /path/to/nixpkgs && nix-build -A nodePackages.<new-or-updated-package>`.
+    To build against a specific Node.js version (e.g. 4.x):
+    `nix-build -A nodePackages_4_x.<new-or-updated-package>`
+ 4. Add and commit all modified and generated files.
+
+For more information about the generation process, consult the
+[README.md](https://github.com/svanderburg/node2nix) file of the `node2nix`
+tool.
diff --git a/doc/languages-frameworks/python.md b/doc/languages-frameworks/python.section.md
index 0f871395854..0f871395854 100644
--- a/doc/languages-frameworks/python.md
+++ b/doc/languages-frameworks/python.section.md
diff --git a/doc/languages-frameworks/r.section.md b/doc/languages-frameworks/r.section.md
new file mode 100644
index 00000000000..c8f02bd1478
--- /dev/null
+++ b/doc/languages-frameworks/r.section.md
@@ -0,0 +1,120 @@
+R packages
+==========
+
+## Installation
+
+Define an environment for R that contains all the libraries that you'd like to
+use by adding the following snippet to your $HOME/.config/nixpkgs/config.nix file:
+
+```nix
+{
+    packageOverrides = super: let self = super.pkgs; in
+    {
+
+        rEnv = super.rWrapper.override {
+            packages = with self.rPackages; [
+                devtools
+                ggplot2
+                reshape2
+                yaml
+                optparse
+                ];
+        };
+    };
+}
+```
+
+Then you can use `nix-env -f "<nixpkgs>" -iA rEnv` to install it into your user
+profile. The set of available libraries can be discovered by running the
+command `nix-env -f "<nixpkgs>" -qaP -A rPackages`. The first column from that
+output is the name that has to be passed to rWrapper in the code snipped above.
+
+However, if you'd like to add a file to your project source to make the
+environment available for other contributors, you can create a `default.nix`
+file like so:
+```nix
+let
+  pkgs = import <nixpkgs> {};
+  stdenv = pkgs.stdenv;
+in with pkgs; {
+  myProject = stdenv.mkDerivation {
+    name = "myProject";
+    version = "1";
+    src = if pkgs.lib.inNixShell then null else nix;
+
+    buildInputs = with rPackages; [
+      R
+      ggplot2
+      knitr
+    ];
+  };
+}
+```
+and then run `nix-shell .` to be dropped into a shell with those packages
+available.
+
+## RStudio
+
+RStudio uses a standard set of packages and ignores any custom R
+environments or installed packages you may have.  To create a custom
+environment, see `rstudioWrapper`, which functions similarly to
+`rWrapper`:
+
+```nix
+{
+    packageOverrides = super: let self = super.pkgs; in
+    {
+
+        rstudioEnv = super.rstudioWrapper.override {
+            packages = with self.rPackages; [
+                dplyr
+                ggplot2
+                reshape2
+                ];
+        };
+    };
+}
+```
+
+Then like above, `nix-env -f "<nixpkgs>" -iA rstudioEnv` will install
+this into your user profile.
+
+Alternatively, you can create a self-contained `shell.nix` without the need to
+modify any configuration files:
+
+```nix
+{ pkgs ? import <nixpkgs> {}
+}:
+
+pkgs.rstudioWrapper.override {
+  packages = with pkgs.rPackages; [ dplyr ggplot2 reshape2 ];
+}
+
+```
+
+Executing `nix-shell` will then drop you into an environment equivalent to the
+one above. If you need additional packages just add them to the list and
+re-enter the shell.
+
+## Updating the package set
+
+```bash
+nix-shell generate-shell.nix
+
+Rscript generate-r-packages.R cran  > cran-packages.nix.new
+mv cran-packages.nix.new cran-packages.nix
+
+Rscript generate-r-packages.R bioc  > bioc-packages.nix.new
+mv bioc-packages.nix.new bioc-packages.nix
+```
+
+`generate-r-packages.R <repo>` reads  `<repo>-packages.nix`, therefor the renaming.
+
+
+## Testing if the Nix-expression could be evaluated
+
+```bash
+nix-build test-evaluation.nix --dry-run
+```
+
+If this exits fine, the expression is ok. If not, you have to edit `default.nix`
diff --git a/doc/languages-frameworks/rust.md b/doc/languages-frameworks/rust.section.md
index f0498eac5b1..f0498eac5b1 100644
--- a/doc/languages-frameworks/rust.md
+++ b/doc/languages-frameworks/rust.section.md
diff --git a/doc/languages-frameworks/vim.md b/doc/languages-frameworks/vim.section.md
index 1d6a4fe8da8..1d6a4fe8da8 100644
--- a/doc/languages-frameworks/vim.md
+++ b/doc/languages-frameworks/vim.section.md
diff --git a/doc/manual.xml b/doc/manual.xml
index eb0a24789d4..385079eb578 100644
--- a/doc/manual.xml
+++ b/doc/manual.xml
@@ -9,7 +9,7 @@
 
   </info>
 
-  <xi:include href="introduction.xml" />
+  <xi:include href="introduction.chapter.xml" />
   <xi:include href="quick-start.xml" />
   <xi:include href="stdenv.xml" />
   <xi:include href="multiple-output.xml" />
diff --git a/doc/shell.md b/doc/shell.section.md
index 079574d4ae8..079574d4ae8 100644
--- a/doc/shell.md
+++ b/doc/shell.section.md