Merge branch 'master' into angerman/mac-fix-recursive-nix

29 files changed, 434 insertions, 158 deletions

diff --git a/doc/manual/src/command-ref/env-common.md b/doc/manual/src/command-ref/env-common.md
index bf00be84f..b4a9bb2a9 100644
--- a/doc/manual/src/command-ref/env-common.md
+++ b/doc/manual/src/command-ref/env-common.md
@@ -71,9 +71,12 @@ Most Nix commands interpret the following environment variables:
     Settings are separated by the newline character.
 
   - <span id="env-NIX_USER_CONF_FILES">[`NIX_USER_CONF_FILES`](#env-NIX_USER_CONF_FILES)</span>\
-    Overrides the location of the user Nix configuration files to load
-    from (defaults to the XDG spec locations). The variable is treated
-    as a list separated by the `:` token.
+    Overrides the location of the Nix user configuration files to load from.
+
+    The default are the locations according to the [XDG Base Directory Specification].
+    See the [XDG Base Directories](#xdg-base-directories) sub-section for details.
+
+    The variable is treated as a list separated by the `:` token.
 
   - <span id="env-TMPDIR">[`TMPDIR`](#env-TMPDIR)</span>\
     Use the specified directory to store temporary files. In particular,
@@ -103,15 +106,19 @@ Most Nix commands interpret the following environment variables:
     384 MiB. Setting it to a low value reduces memory consumption, but
     will increase runtime due to the overhead of garbage collection.
 
-## XDG Base Directory
+## XDG Base Directories
+
+Nix follows the [XDG Base Directory Specification].
+
+For backwards compatibility, Nix commands will follow the standard only when [`use-xdg-base-directories`] is enabled.
+[New Nix commands](@docroot@/command-ref/new-cli/nix.md) (experimental) conform to the standard by default.
 
-New Nix commands conform to the [XDG Base Directory Specification], and use the following environment variables to determine locations of various state and configuration files:
+The following environment variables are used to determine locations of various state and configuration files:
 
 - [`XDG_CONFIG_HOME`]{#env-XDG_CONFIG_HOME} (default `~/.config`)
 - [`XDG_STATE_HOME`]{#env-XDG_STATE_HOME} (default `~/.local/state`)
 - [`XDG_CACHE_HOME`]{#env-XDG_CACHE_HOME} (default `~/.cache`)
 
-Classic Nix commands can also be made to follow this standard using the [`use-xdg-base-directories`] configuration option.
 
 [XDG Base Directory Specification]: https://specifications.freedesktop.org/basedir-spec/basedir-spec-latest.html
-[`use-xdg-base-directories`]: @docroot@/command-ref/conf-file.md#conf-use-xdg-base-directories
\ No newline at end of file
+[`use-xdg-base-directories`]: @docroot@/command-ref/conf-file.md#conf-use-xdg-base-directories
diff --git a/doc/manual/src/command-ref/files/channels.md b/doc/manual/src/command-ref/files/channels.md
new file mode 100644
index 000000000..7b1f27128
--- /dev/null
+++ b/doc/manual/src/command-ref/files/channels.md
@@ -0,0 +1,26 @@
+## Channels
+
+A directory containing symlinks to Nix channels, managed by [`nix-channel`]:
+
+- `$XDG_STATE_HOME/nix/profiles/channels` for regular users
+- `$NIX_STATE_DIR/profiles/per-user/root/channels` for `root`
+
+[`nix-channel`] uses a [profile](@docroot@/command-ref/files/profiles.md) to store channels.
+This profile contains symlinks to the contents of those channels.
+
+## Subscribed channels
+
+The list of subscribed channels is stored in
+
+- `~/.nix-channels`
+- `$XDG_STATE_HOME/nix/channels` if [`use-xdg-base-directories`] is set to `true`
+
+in the following format:
+
+```
+<url> <name>
+...
+```
+
+[`nix-channel`]: @docroot@/command-ref/nix-channel.md
+[`use-xdg-base-directories`]: @docroot@/command-ref/conf-file.md#conf-use-xdg-base-directories
diff --git a/doc/manual/src/command-ref/files/default-nix-expression.md b/doc/manual/src/command-ref/files/default-nix-expression.md
new file mode 100644
index 000000000..620f7035c
--- /dev/null
+++ b/doc/manual/src/command-ref/files/default-nix-expression.md
@@ -0,0 +1,52 @@
+## Default Nix expression
+
+The source for the default [Nix expressions](@docroot@/language/index.md) used by [`nix-env`]:
+
+- `~/.nix-defexpr`
+- `$XDG_STATE_HOME/nix/defexpr` if [`use-xdg-base-directories`] is set to `true`.
+
+It is loaded as follows:
+
+- If the default expression is a file, it is loaded as a Nix expression.
+- If the default expression is a directory containing a `default.nix` file, that `default.nix` file is loaded as a Nix expression.
+- If the default expression is a directory without a `default.nix` file, then its contents (both files and subdirectories) are loaded as Nix expressions.
+  The expressions are combined into a single attribute set, each expression under an attribute with the same name as the original file or subdirectory.
+  Subdirectories without a `default.nix` file are traversed recursively in search of more Nix expressions, but the names of these intermediate directories are not added to the attribute paths of the default Nix expression.
+
+Then, the resulting expression is interpreted like this:
+
+- If the expression is an attribute set, it is used as the default Nix expression.
+- If the expression is a function, an empty set is passed as argument and the return value is used as the default Nix expression.
+
+
+For example, if the default expression contains two files, `foo.nix` and `bar.nix`, then the default Nix expression will be equivalent to
+
+```nix
+{
+  foo = import ~/.nix-defexpr/foo.nix;
+  bar = import ~/.nix-defexpr/bar.nix;
+}
+```
+
+The file [`manifest.nix`](@docroot@/command-ref/files/manifest.nix.md) is always ignored.
+
+The command [`nix-channel`] places a symlink to the user's current [channels profile](@docroot@/command-ref/files/channels.md) in this directory.
+This makes all subscribed channels available as attributes in the default expression.
+
+## User channel link
+
+A symlink that ensures that [`nix-env`] can find your channels:
+
+- `~/.nix-defexpr/channels`
+- `$XDG_STATE_HOME/defexpr/channels` if [`use-xdg-base-directories`] is set to `true`.
+
+This symlink points to:
+
+- `$XDG_STATE_HOME/profiles/channels` for regular users
+- `$NIX_STATE_DIR/profiles/per-user/root/channels` for `root`
+
+In a multi-user installation, you may also have `~/.nix-defexpr/channels_root`, which links to the channels of the root user.[`nix-env`]: ../nix-env.md
+
+[`nix-env`]: @docroot@/command-ref/nix-env.md
+[`nix-channel`]: @docroot@/command-ref/nix-channel.md
+[`use-xdg-base-directories`]: @docroot@/command-ref/conf-file.md#conf-use-xdg-base-directories
diff --git a/doc/manual/src/command-ref/files/manifest.json.md b/doc/manual/src/command-ref/files/manifest.json.md
new file mode 100644
index 000000000..bcfe7373d
--- /dev/null
+++ b/doc/manual/src/command-ref/files/manifest.json.md
@@ -0,0 +1,45 @@
+## `manifest.json`
+
+The manifest file records the provenance of the packages that are installed in a [profile](./profiles.md) managed by [`nix profile`](@docroot@/command-ref/new-cli/nix3-profile.md) (experimental).
+
+Here is an example of what the file might look like after installing `zoom-us` from Nixpkgs:
+
+```json
+{
+  "version": 1,
+  "elements": [
+    {
+      "active": true,
+      "attrPath": "legacyPackages.x86_64-linux.zoom-us",
+      "originalUrl": "flake:nixpkgs",
+      "storePaths": [
+        "/nix/store/wbhg2ga8f3h87s9h5k0slxk0m81m4cxl-zoom-us-5.3.469451.0927"
+      ],
+      "uri": "github:NixOS/nixpkgs/13d0c311e3ae923a00f734b43fd1d35b47d8943a"
+    },
+    …
+  ]
+}
+```
+
+Each object in the array `elements` denotes an installed package and
+has the following fields:
+
+* `originalUrl`: The [flake reference](@docroot@/command-ref/new-cli/nix3-flake.md) specified by
+  the user at the time of installation (e.g. `nixpkgs`). This is also
+  the flake reference that will be used by `nix profile upgrade`.
+
+* `uri`: The locked flake reference to which `originalUrl` resolved.
+
+* `attrPath`: The flake output attribute that provided this
+  package. Note that this is not necessarily the attribute that the
+  user specified, but the one resulting from applying the default
+  attribute paths and prefixes; for instance, `hello` might resolve to
+  `packages.x86_64-linux.hello` and the empty string to
+  `packages.x86_64-linux.default`.
+
+* `storePath`: The paths in the Nix store containing the package.
+
+* `active`: Whether the profile contains symlinks to the files of this
+  package. If set to false, the package is kept in the Nix store, but
+  is not "visible" in the profile's symlink tree.
diff --git a/doc/manual/src/command-ref/files/manifest.nix.md b/doc/manual/src/command-ref/files/manifest.nix.md
new file mode 100644
index 000000000..d7d1b605b
--- /dev/null
+++ b/doc/manual/src/command-ref/files/manifest.nix.md
@@ -0,0 +1,128 @@
+## `manifest.nix`
+
+The manifest file records the provenance of the packages that are installed in a [profile](./profiles.md) managed by [`nix-env`](@docroot@/command-ref/nix-env.md).
+
+Here is an example of how this file might look like after installing `hello` from Nixpkgs:
+
+```nix
+[{
+  meta = {
+    available = true;
+    broken = false;
+    changelog =
+      "https://git.savannah.gnu.org/cgit/hello.git/plain/NEWS?h=v2.12.1";
+    description = "A program that produces a familiar, friendly greeting";
+    homepage = "https://www.gnu.org/software/hello/manual/";
+    insecure = false;
+    license = {
+      deprecated = false;
+      free = true;
+      fullName = "GNU General Public License v3.0 or later";
+      redistributable = true;
+      shortName = "gpl3Plus";
+      spdxId = "GPL-3.0-or-later";
+      url = "https://spdx.org/licenses/GPL-3.0-or-later.html";
+    };
+    longDescription = ''
+      GNU Hello is a program that prints "Hello, world!" when you run it.
+      It is fully customizable.
+    '';
+    maintainers = [{
+      email = "edolstra+nixpkgs@gmail.com";
+      github = "edolstra";
+      githubId = 1148549;
+      name = "Eelco Dolstra";
+    }];
+    name = "hello-2.12.1";
+    outputsToInstall = [ "out" ];
+    platforms = [
+      "i686-cygwin"
+      "x86_64-cygwin"
+      "x86_64-darwin"
+      "i686-darwin"
+      "aarch64-darwin"
+      "armv7a-darwin"
+      "i686-freebsd13"
+      "x86_64-freebsd13"
+      "aarch64-genode"
+      "i686-genode"
+      "x86_64-genode"
+      "x86_64-solaris"
+      "js-ghcjs"
+      "aarch64-linux"
+      "armv5tel-linux"
+      "armv6l-linux"
+      "armv7a-linux"
+      "armv7l-linux"
+      "i686-linux"
+      "m68k-linux"
+      "microblaze-linux"
+      "microblazeel-linux"
+      "mipsel-linux"
+      "mips64el-linux"
+      "powerpc64-linux"
+      "powerpc64le-linux"
+      "riscv32-linux"
+      "riscv64-linux"
+      "s390-linux"
+      "s390x-linux"
+      "x86_64-linux"
+      "mmix-mmixware"
+      "aarch64-netbsd"
+      "armv6l-netbsd"
+      "armv7a-netbsd"
+      "armv7l-netbsd"
+      "i686-netbsd"
+      "m68k-netbsd"
+      "mipsel-netbsd"
+      "powerpc-netbsd"
+      "riscv32-netbsd"
+      "riscv64-netbsd"
+      "x86_64-netbsd"
+      "aarch64_be-none"
+      "aarch64-none"
+      "arm-none"
+      "armv6l-none"
+      "avr-none"
+      "i686-none"
+      "microblaze-none"
+      "microblazeel-none"
+      "msp430-none"
+      "or1k-none"
+      "m68k-none"
+      "powerpc-none"
+      "powerpcle-none"
+      "riscv32-none"
+      "riscv64-none"
+      "rx-none"
+      "s390-none"
+      "s390x-none"
+      "vc4-none"
+      "x86_64-none"
+      "i686-openbsd"
+      "x86_64-openbsd"
+      "x86_64-redox"
+      "wasm64-wasi"
+      "wasm32-wasi"
+      "x86_64-windows"
+      "i686-windows"
+    ];
+    position =
+      "/nix/store/7niq32w715567hbph0q13m5lqna64c1s-nixos-unstable.tar.gz/nixos-unstable.tar.gz/pkgs/applications/misc/hello/default.nix:34";
+    unfree = false;
+    unsupported = false;
+  };
+  name = "hello-2.12.1";
+  out = {
+    outPath = "/nix/store/260q5867crm1xjs4khgqpl6vr9kywql1-hello-2.12.1";
+  };
+  outPath = "/nix/store/260q5867crm1xjs4khgqpl6vr9kywql1-hello-2.12.1";
+  outputs = [ "out" ];
+  system = "x86_64-linux";
+  type = "derivation";
+}]
+```
+
+Each element in this list corresponds to an installed package.
+It incorporates some attributes of the original derivation, including `meta`, `name`, `out`, `outPath`, `outputs`, `system`.
+This information is used by Nix for querying and updating the package.
diff --git a/doc/manual/src/command-ref/files/profiles.md b/doc/manual/src/command-ref/files/profiles.md
new file mode 100644
index 000000000..b5c737880
--- /dev/null
+++ b/doc/manual/src/command-ref/files/profiles.md
@@ -0,0 +1,74 @@
+## Profiles
+
+A directory that contains links to profiles managed by [`nix-env`] and [`nix profile`]:
+
+- `$XDG_STATE_HOME/nix/profiles` for regular users
+- `$NIX_STATE_DIR/profiles/per-user/root` if the user is `root`
+
+A profile is a directory of symlinks to files in the Nix store.
+
+### Filesystem layout
+
+Profiles are versioned as follows. When using a profile named *path*, *path* is a symlink to *path*`-`*N*`-link`, where *N* is the version of the profile.
+In turn, *path*`-`*N*`-link` is a symlink to a path in the Nix store.
+For example:
+
+```console
+$ ls -l ~alice/.local/state/nix/profiles/profile*
+lrwxrwxrwx 1 alice users 14 Nov 25 14:35 /home/alice/.local/state/nix/profiles/profile -> profile-7-link
+lrwxrwxrwx 1 alice users 51 Oct 28 16:18 /home/alice/.local/state/nix/profiles/profile-5-link -> /nix/store/q69xad13ghpf7ir87h0b2gd28lafjj1j-profile
+lrwxrwxrwx 1 alice users 51 Oct 29 13:20 /home/alice/.local/state/nix/profiles/profile-6-link -> /nix/store/6bvhpysd7vwz7k3b0pndn7ifi5xr32dg-profile
+lrwxrwxrwx 1 alice users 51 Nov 25 14:35 /home/alice/.local/state/nix/profiles/profile-7-link -> /nix/store/mp0x6xnsg0b8qhswy6riqvimai4gm677-profile
+```
+
+Each of these symlinks is a root for the Nix garbage collector.
+
+The contents of the store path corresponding to each version of the
+profile is a tree of symlinks to the files of the installed packages,
+e.g.
+
+```console
+$ ll -R ~eelco/.local/state/nix/profiles/profile-7-link/
+/home/eelco/.local/state/nix/profiles/profile-7-link/:
+total 20
+dr-xr-xr-x 2 root root 4096 Jan  1  1970 bin
+-r--r--r-- 2 root root 1402 Jan  1  1970 manifest.nix
+dr-xr-xr-x 4 root root 4096 Jan  1  1970 share
+
+/home/eelco/.local/state/nix/profiles/profile-7-link/bin:
+total 20
+lrwxrwxrwx 5 root root 79 Jan  1  1970 chromium -> /nix/store/ijm5k0zqisvkdwjkc77mb9qzb35xfi4m-chromium-86.0.4240.111/bin/chromium
+lrwxrwxrwx 7 root root 87 Jan  1  1970 spotify -> /nix/store/w9182874m1bl56smps3m5zjj36jhp3rn-spotify-1.1.26.501.gbe11e53b-15/bin/spotify
+lrwxrwxrwx 3 root root 79 Jan  1  1970 zoom-us -> /nix/store/wbhg2ga8f3h87s9h5k0slxk0m81m4cxl-zoom-us-5.3.469451.0927/bin/zoom-us
+
+/home/eelco/.local/state/nix/profiles/profile-7-link/share/applications:
+total 12
+lrwxrwxrwx 4 root root 120 Jan  1  1970 chromium-browser.desktop -> /nix/store/4cf803y4vzfm3gyk3vzhzb2327v0kl8a-chromium-unwrapped-86.0.4240.111/share/applications/chromium-browser.desktop
+lrwxrwxrwx 7 root root 110 Jan  1  1970 spotify.desktop -> /nix/store/w9182874m1bl56smps3m5zjj36jhp3rn-spotify-1.1.26.501.gbe11e53b-15/share/applications/spotify.desktop
+lrwxrwxrwx 3 root root 107 Jan  1  1970 us.zoom.Zoom.desktop -> /nix/store/wbhg2ga8f3h87s9h5k0slxk0m81m4cxl-zoom-us-5.3.469451.0927/share/applications/us.zoom.Zoom.desktop
+
+…
+```
+
+Each profile version contains a manifest file:
+- [`manifest.nix`](@docroot@/command-ref/files/manifest.nix.md) used by [`nix-env`](@docroot@/command-ref/nix-env.md).
+- [`manifest.json`](@docroot@/command-ref/files/manifest.json.md) used by [`nix profile`](@docroot@/command-ref/new-cli/nix3-profile.md) (experimental).
+
+## User profile link
+
+A symbolic link to the user's current profile:
+
+- `~/.nix-profile`
+- `$XDG_STATE_HOME/nix/profile` if [`use-xdg-base-directories`] is set to `true`.
+
+By default, this symlink points to:
+
+- `$XDG_STATE_HOME/nix/profiles/profile` for regular users
+- `$NIX_STATE_DIR/profiles/per-user/root/profile` for `root`
+
+The `PATH` environment variable should include `/bin` subdirectory of the profile link (e.g. `~/.nix-profile/bin`) for the user environment to be visible to the user.
+The [installer](@docroot@/installation/installing-binary.md) sets this up by default, unless you enable [`use-xdg-base-directories`].
+
+[`nix-env`]: @docroot@/command-ref/nix-env.md
+[`nix profile`]: @docroot@/command-ref/new-cli/nix3-profile.md
+[`use-xdg-base-directories`]: @docroot@/command-ref/conf-file.md#conf-use-xdg-base-directories
diff --git a/doc/manual/src/command-ref/nix-build.md b/doc/manual/src/command-ref/nix-build.md
index 44de4cf53..f70bbd7f2 100644
--- a/doc/manual/src/command-ref/nix-build.md
+++ b/doc/manual/src/command-ref/nix-build.md
@@ -76,7 +76,7 @@ except for `--arg` and `--attr` / `-A` which are passed to `nix-instantiate`.
 # Examples
 
 ```console
-$ nix-build '<nixpkgs>' -A firefox
+$ nix-build '<nixpkgs>' --attr firefox
 store derivation is /nix/store/qybprl8sz2lc...-firefox-1.5.0.7.drv
 /nix/store/d18hyl92g30l...-firefox-1.5.0.7
 
@@ -91,7 +91,7 @@ If a derivation has multiple outputs, `nix-build` will build the default
 (first) output. You can also build all outputs:
 
 ```console
-$ nix-build '<nixpkgs>' -A openssl.all
+$ nix-build '<nixpkgs>' --attr openssl.all
 ```
 
 This will create a symlink for each output named `result-outputname`.
@@ -101,7 +101,7 @@ outputs `out`, `bin` and `man`, `nix-build` will create symlinks
 specific output:
 
 ```console
-$ nix-build '<nixpkgs>' -A openssl.man
+$ nix-build '<nixpkgs>' --attr openssl.man
 ```
 
 This will create a symlink `result-man`.
@@ -109,7 +109,7 @@ This will create a symlink `result-man`.
 Build a Nix expression given on the command line:
 
 ```console
-$ nix-build -E 'with import <nixpkgs> { }; runCommand "foo" { } "echo bar > $out"'
+$ nix-build --expr 'with import <nixpkgs> { }; runCommand "foo" { } "echo bar > $out"'
 $ cat ./result
 bar
 ```
@@ -118,5 +118,5 @@ Build the GNU Hello package from the latest revision of the master
 branch of Nixpkgs:
 
 ```console
-$ nix-build https://github.com/NixOS/nixpkgs/archive/master.tar.gz -A hello
+$ nix-build https://github.com/NixOS/nixpkgs/archive/master.tar.gz --attr hello
 ```
diff --git a/doc/manual/src/command-ref/nix-channel.md b/doc/manual/src/command-ref/nix-channel.md
index 2027cc98d..a210583ae 100644
--- a/doc/manual/src/command-ref/nix-channel.md
+++ b/doc/manual/src/command-ref/nix-channel.md
@@ -22,6 +22,9 @@ This command has the following operations:
     channels. If *name* is omitted, it defaults to the last component of
     *url*, with the suffixes `-stable` or `-unstable` removed.
 
+    A channel URL must point to a directory containing a file `nixexprs.tar.gz`.
+    At the top level, that tarball must contain a single directory with a `default.nix` file that serves as the channel’s entry point.
+
   - `--remove` *name*\
     Removes the channel named *name* from the list of subscribed
     channels.
@@ -49,6 +52,12 @@ The list of subscribed channels is stored in `~/.nix-channels`.
 
 {{#include ./env-common.md}}
 
+# Files
+
+`nix-channel` operates on the following files.
+
+{{#include ./files/channels.md}}
+
 # Examples
 
 To subscribe to the Nixpkgs channel and install the GNU Hello package:
@@ -56,45 +65,18 @@ To subscribe to the Nixpkgs channel and install the GNU Hello package:
 ```console
 $ nix-channel --add https://nixos.org/channels/nixpkgs-unstable
 $ nix-channel --update
-$ nix-env -iA nixpkgs.hello
+$ nix-env --install --attr nixpkgs.hello
 ```
 
 You can revert channel updates using `--rollback`:
 
 ```console
-$ nix-instantiate --eval -E '(import <nixpkgs> {}).lib.version'
+$ nix-instantiate --eval --expr '(import <nixpkgs> {}).lib.version'
 "14.04.527.0e935f1"
 
 $ nix-channel --rollback
 switching from generation 483 to 482
 
-$ nix-instantiate --eval -E '(import <nixpkgs> {}).lib.version'
+$ nix-instantiate --eval --expr '(import <nixpkgs> {}).lib.version'
 "14.04.526.dbadfad"
 ```
-
-# Files
-
-  - `${XDG_STATE_HOME-$HOME/.local/state}/nix/profiles/channels`\
-    `nix-channel` uses a `nix-env` profile to keep track of previous
-    versions of the subscribed channels. Every time you run `nix-channel
-    --update`, a new channel generation (that is, a symlink to the
-    channel Nix expressions in the Nix store) is created. This enables
-    `nix-channel --rollback` to revert to previous versions.
-
-  - `~/.nix-defexpr/channels`\
-    This is a symlink to
-    `${XDG_STATE_HOME-$HOME/.local/state}/nix/profiles/channels`. It ensures that
-    `nix-env` can find your channels. In a multi-user installation, you
-    may also have `~/.nix-defexpr/channels_root`, which links to the
-    channels of the root user.
-
-# Channel format
-
-A channel URL should point to a directory containing the following
-files:
-
-  - `nixexprs.tar.xz`\
-    A tarball containing Nix expressions and files referenced by them
-    (such as build scripts and patches). At the top level, the tarball
-    should contain a single directory. That directory must contain a
-    file `default.nix` that serves as the channel’s “entry point”.
diff --git a/doc/manual/src/command-ref/nix-copy-closure.md b/doc/manual/src/command-ref/nix-copy-closure.md
index 0801e8246..fbf6828da 100644
--- a/doc/manual/src/command-ref/nix-copy-closure.md
+++ b/doc/manual/src/command-ref/nix-copy-closure.md
@@ -87,5 +87,5 @@ environment:
 ```console
 $ nix-copy-closure --from alice@itchy.labs \
     /nix/store/0dj0503hjxy5mbwlafv1rsbdiyx1gkdy-subversion-1.4.4
-$ nix-env -i /nix/store/0dj0503hjxy5mbwlafv1rsbdiyx1gkdy-subversion-1.4.4
+$ nix-env --install /nix/store/0dj0503hjxy5mbwlafv1rsbdiyx1gkdy-subversion-1.4.4
 ```
diff --git a/doc/manual/src/command-ref/nix-env.md b/doc/manual/src/command-ref/nix-env.md
index 42b5bca77..941723216 100644
--- a/doc/manual/src/command-ref/nix-env.md
+++ b/doc/manual/src/command-ref/nix-env.md
@@ -49,7 +49,7 @@ These pages can be viewed offline:
 
 # Selectors
 
-Several commands, such as `nix-env -q` and `nix-env -i`, take a list of
+Several commands, such as `nix-env --query ` and `nix-env --install `, take a list of
 arguments that specify the packages on which to operate. These are
 extended regular expressions that must match the entire name of the
 package. (For details on regular expressions, see **regex**(7).) The match is
@@ -83,46 +83,8 @@ match. Here are some examples:
 
 # Files
 
-  - `~/.nix-defexpr`\
-    The source for the default Nix expressions used by the
-    `--install`, `--upgrade`, and `--query --available` operations to
-    obtain derivations. The `--file` option may be used to override
-    this default.
-
-    If `~/.nix-defexpr` is a file, it is loaded as a Nix expression. If
-    the expression is a set, it is used as the default Nix expression.
-    If the expression is a function, an empty set is passed as argument
-    and the return value is used as the default Nix expression.
-
-    If `~/.nix-defexpr` is a directory containing a `default.nix` file,
-    that file is loaded as in the above paragraph.
-
-    If `~/.nix-defexpr` is a directory without a `default.nix` file,
-    then its contents (both files and subdirectories) are loaded as Nix
-    expressions. The expressions are combined into a single set, each
-    expression under an attribute with the same name as the original
-    file or subdirectory.
-
-    For example, if `~/.nix-defexpr` contains two files, `foo.nix` and
-    `bar.nix`, then the default Nix expression will essentially be
-
-    ```nix
-    {
-      foo = import ~/.nix-defexpr/foo.nix;
-      bar = import ~/.nix-defexpr/bar.nix;
-    }
-    ```
-
-    The file `manifest.nix` is always ignored. Subdirectories without a
-    `default.nix` file are traversed recursively in search of more Nix
-    expressions, but the names of these intermediate directories are not
-    added to the attribute paths of the default Nix expression.
-
-    The command `nix-channel` places symlinks to the downloaded Nix
-    expressions from each subscribed channel in this directory.
-
-  - `~/.nix-profile`\
-    A symbolic link to the user's current profile. By default, this
-    symlink points to `prefix/var/nix/profiles/default`. The `PATH`
-    environment variable should include `~/.nix-profile/bin` for the
-    user environment to be visible to the user.
+`nix-env` operates on the following files.
+
+{{#include ./files/default-nix-expression.md}}
+
+{{#include ./files/profiles.md}}
diff --git a/doc/manual/src/command-ref/nix-env/delete-generations.md b/doc/manual/src/command-ref/nix-env/delete-generations.md
index 6f0af5384..92cb7f0d9 100644
--- a/doc/manual/src/command-ref/nix-env/delete-generations.md
+++ b/doc/manual/src/command-ref/nix-env/delete-generations.md
@@ -41,6 +41,6 @@ $ nix-env --delete-generations 30d
 ```
 
 ```console
-$ nix-env -p other_profile --delete-generations old
+$ nix-env --profile other_profile --delete-generations old
 ```
 
diff --git a/doc/manual/src/command-ref/nix-env/install.md b/doc/manual/src/command-ref/nix-env/install.md
index d754accfe..ad179cbc7 100644
--- a/doc/manual/src/command-ref/nix-env/install.md
+++ b/doc/manual/src/command-ref/nix-env/install.md
@@ -36,7 +36,7 @@ a number of possible ways:
     then the derivation with the highest version will be installed.
 
     You can force the installation of multiple derivations with the same
-    name by being specific about the versions. For instance, `nix-env -i
+    name by being specific about the versions. For instance, `nix-env --install
     gcc-3.3.6 gcc-4.1.1` will install both version of GCC (and will
     probably cause a user environment conflict\!).
 
@@ -44,7 +44,7 @@ a number of possible ways:
     paths* that select attributes from the top-level Nix
     expression. This is faster than using derivation names and
     unambiguous. To find out the attribute paths of available
-    packages, use `nix-env -qaP`.
+    packages, use `nix-env --query --available --attr-path `.
 
   - If `--from-profile` *path* is given, *args* is a set of names
     denoting installed store paths in the profile *path*. This is an
@@ -87,7 +87,7 @@ a number of possible ways:
 
   - `--remove-all` / `-r`\
     Remove all previously installed packages first. This is equivalent
-    to running `nix-env -e '.*'` first, except that everything happens
+    to running `nix-env --uninstall '.*'` first, except that everything happens
     in a single transaction.
 
 {{#include ./opt-common.md}}
@@ -103,9 +103,9 @@ a number of possible ways:
 To install a package using a specific attribute path from the active Nix expression:
 
 ```console
-$ nix-env -iA gcc40mips
+$ nix-env --install --attr gcc40mips
 installing `gcc-4.0.2'
-$ nix-env -iA xorg.xorgserver
+$ nix-env --install --attr xorg.xorgserver
 installing `xorg-server-1.2.0'
 ```
 
@@ -133,32 +133,32 @@ installing `gcc-3.3.2'
 To install all derivations in the Nix expression `foo.nix`:
 
 ```console
-$ nix-env -f ~/foo.nix -i '.*'
+$ nix-env --file ~/foo.nix --install '.*'
 ```
 
 To copy the store path with symbolic name `gcc` from another profile:
 
 ```console
-$ nix-env -i --from-profile /nix/var/nix/profiles/foo gcc
+$ nix-env --install --from-profile /nix/var/nix/profiles/foo gcc
 ```
 
 To install a specific [store derivation] (typically created by
 `nix-instantiate`):
 
 ```console
-$ nix-env -i /nix/store/fibjb1bfbpm5mrsxc4mh2d8n37sxh91i-gcc-3.4.3.drv
+$ nix-env --install /nix/store/fibjb1bfbpm5mrsxc4mh2d8n37sxh91i-gcc-3.4.3.drv
 ```
 
 To install a specific output path:
 
 ```console
-$ nix-env -i /nix/store/y3cgx0xj1p4iv9x0pnnmdhr8iyg741vk-gcc-3.4.3
+$ nix-env --install /nix/store/y3cgx0xj1p4iv9x0pnnmdhr8iyg741vk-gcc-3.4.3
 ```
 
 To install from a Nix expression specified on the command-line:
 
 ```console
-$ nix-env -f ./foo.nix -i -E \
+$ nix-env --file ./foo.nix --install --expr \
     'f: (f {system = "i686-linux";}).subversionWithJava'
 ```
 
@@ -170,7 +170,7 @@ function defined in `./foo.nix`.
 A dry-run tells you which paths will be downloaded or built from source:
 
 ```console
-$ nix-env -f '<nixpkgs>' -iA hello --dry-run
+$ nix-env --file '<nixpkgs>' --install --attr hello --dry-run
 (dry run; not doing anything)
 installing ‘hello-2.10’
 this path will be fetched (0.04 MiB download, 0.19 MiB unpacked):
@@ -182,6 +182,6 @@ To install Firefox from the latest revision in the Nixpkgs/NixOS 14.12
 channel:
 
 ```console
-$ nix-env -f https://github.com/NixOS/nixpkgs/archive/nixos-14.12.tar.gz -iA firefox
+$ nix-env --file https://github.com/NixOS/nixpkgs/archive/nixos-14.12.tar.gz --install --attr firefox
 ```
 
diff --git a/doc/manual/src/command-ref/nix-env/query.md b/doc/manual/src/command-ref/nix-env/query.md
index 18f0ee210..c9b4d8513 100644
--- a/doc/manual/src/command-ref/nix-env/query.md
+++ b/doc/manual/src/command-ref/nix-env/query.md
@@ -137,7 +137,7 @@ derivation is shown unless `--no-name` is specified.
 To show installed packages:
 
 ```console
-$ nix-env -q
+$ nix-env --query
 bison-1.875c
 docbook-xml-4.2
 firefox-1.0.4
@@ -149,7 +149,7 @@ ORBit2-2.8.3
 To show available packages:
 
 ```console
-$ nix-env -qa
+$ nix-env --query --available
 firefox-1.0.7
 GConf-2.4.0.1
 MPlayer-1.0pre7
@@ -160,7 +160,7 @@ ORBit2-2.8.3
 To show the status of available packages:
 
 ```console
-$ nix-env -qas
+$ nix-env --query --available --status
 -P- firefox-1.0.7   (not installed but present)
 --S GConf-2.4.0.1   (not present, but there is a substitute for fast installation)
 --S MPlayer-1.0pre3 (i.e., this is not the installed MPlayer, even though the version is the same!)
@@ -171,14 +171,14 @@ IP- ORBit2-2.8.3    (installed and by definition present)
 To show available packages in the Nix expression `foo.nix`:
 
 ```console
-$ nix-env -f ./foo.nix -qa
+$ nix-env --file ./foo.nix --query --available
 foo-1.2.3
 ```
 
 To compare installed versions to what’s available:
 
 ```console
-$ nix-env -qc
+$ nix-env --query --compare-versions
 ...
 acrobat-reader-7.0 - ?      (package is not available at all)
 autoconf-2.59      = 2.59   (same version)
@@ -189,7 +189,7 @@ firefox-1.0.4      < 1.0.7  (a more recent version is available)
 To show all packages with “`zip`” in the name:
 
 ```console
-$ nix-env -qa '.*zip.*'
+$ nix-env --query --available '.*zip.*'
 bzip2-1.0.6
 gzip-1.6
 zip-3.0
@@ -199,7 +199,7 @@ zip-3.0
 To show all packages with “`firefox`” or “`chromium`” in the name:
 
 ```console
-$ nix-env -qa '.*(firefox|chromium).*'
+$ nix-env --query --available '.*(firefox|chromium).*'
 chromium-37.0.2062.94
 chromium-beta-38.0.2125.24
 firefox-32.0.3
@@ -210,6 +210,6 @@ firefox-with-plugins-13.0.1
 To show all packages in the latest revision of the Nixpkgs repository:
 
 ```console
-$ nix-env -f https://github.com/NixOS/nixpkgs/archive/master.tar.gz -qa
+$ nix-env --file https://github.com/NixOS/nixpkgs/archive/master.tar.gz --query --available
 ```
 
diff --git a/doc/manual/src/command-ref/nix-env/set-flag.md b/doc/manual/src/command-ref/nix-env/set-flag.md
index 63f0a0ff9..e04b22a91 100644
--- a/doc/manual/src/command-ref/nix-env/set-flag.md
+++ b/doc/manual/src/command-ref/nix-env/set-flag.md
@@ -46,16 +46,16 @@ To prevent the currently installed Firefox from being upgraded:
 $ nix-env --set-flag keep true firefox
 ```
 
-After this, `nix-env -u` will ignore Firefox.
+After this, `nix-env --upgrade ` will ignore Firefox.
 
 To disable the currently installed Firefox, then install a new Firefox
 while the old remains part of the profile:
 
 ```console
-$ nix-env -q
+$ nix-env --query
 firefox-2.0.0.9 (the current one)
 
-$ nix-env --preserve-installed -i firefox-2.0.0.11
+$ nix-env --preserve-installed --install firefox-2.0.0.11
 installing `firefox-2.0.0.11'
 building path(s) `/nix/store/myy0y59q3ig70dgq37jqwg1j0rsapzsl-user-environment'
 collision between `/nix/store/...-firefox-2.0.0.11/bin/firefox'
@@ -65,10 +65,10 @@ collision between `/nix/store/...-firefox-2.0.0.11/bin/firefox'
 $ nix-env --set-flag active false firefox
 setting flag on `firefox-2.0.0.9'
 
-$ nix-env --preserve-installed -i firefox-2.0.0.11
+$ nix-env --preserve-installed --install firefox-2.0.0.11
 installing `firefox-2.0.0.11'
 
-$ nix-env -q
+$ nix-env --query
 firefox-2.0.0.11 (the enabled one)
 firefox-2.0.0.9 (the disabled one)
 ```
diff --git a/doc/manual/src/command-ref/nix-env/set.md b/doc/manual/src/command-ref/nix-env/set.md
index c1cf75739..b9950eeab 100644
--- a/doc/manual/src/command-ref/nix-env/set.md
+++ b/doc/manual/src/command-ref/nix-env/set.md
@@ -25,6 +25,6 @@ The following updates a profile such that its current generation will
 contain just Firefox:
 
 ```console
-$ nix-env -p /nix/var/nix/profiles/browser --set firefox
+$ nix-env --profile /nix/var/nix/profiles/browser --set firefox
 ```
 
diff --git a/doc/manual/src/command-ref/nix-env/switch-generation.md b/doc/manual/src/command-ref/nix-env/switch-generation.md
index e550325c4..38cf0534d 100644
--- a/doc/manual/src/command-ref/nix-env/switch-generation.md
+++ b/doc/manual/src/command-ref/nix-env/switch-generation.md
@@ -27,7 +27,7 @@ Switching will fail if the specified generation does not exist.
 # Examples
 
 ```console
-$ nix-env -G 42
+$ nix-env --switch-generation 42
 switching from generation 50 to 42
 ```
 
diff --git a/doc/manual/src/command-ref/nix-env/switch-profile.md b/doc/manual/src/command-ref/nix-env/switch-profile.md
index b389e4140..5ae2fdced 100644
--- a/doc/manual/src/command-ref/nix-env/switch-profile.md
+++ b/doc/manual/src/command-ref/nix-env/switch-profile.md
@@ -22,5 +22,5 @@ the symlink `~/.nix-profile` is made to point to *path*.
 # Examples
 
 ```console
-$ nix-env -S ~/my-profile
+$ nix-env --switch-profile ~/my-profile
 ```
diff --git a/doc/manual/src/command-ref/nix-env/uninstall.md b/doc/manual/src/command-ref/nix-env/uninstall.md
index e9ec8a15e..734cc7675 100644
--- a/doc/manual/src/command-ref/nix-env/uninstall.md
+++ b/doc/manual/src/command-ref/nix-env/uninstall.md
@@ -24,5 +24,5 @@ designated by the symbolic names *drvnames* are removed.
 
 ```console
 $ nix-env --uninstall gcc
-$ nix-env -e '.*' (remove everything)
+$ nix-env --uninstall '.*' (remove everything)
 ```
diff --git a/doc/manual/src/command-ref/nix-env/upgrade.md b/doc/manual/src/command-ref/nix-env/upgrade.md
index f88ffcbee..322dfbda2 100644
--- a/doc/manual/src/command-ref/nix-env/upgrade.md
+++ b/doc/manual/src/command-ref/nix-env/upgrade.md
@@ -76,21 +76,21 @@ version is installed.
 # Examples
 
 ```console
-$ nix-env --upgrade -A nixpkgs.gcc
+$ nix-env --upgrade --attr nixpkgs.gcc
 upgrading `gcc-3.3.1' to `gcc-3.4'
 ```
 
 When there are no updates available, nothing will happen:
 
 ```console
-$ nix-env --upgrade -A nixpkgs.pan
+$ nix-env --upgrade --attr nixpkgs.pan
 ```
 
 Using `-A` is preferred when possible, as it is faster and unambiguous but
 it is also possible to upgrade to a specific version by matching the derivation name:
 
 ```console
-$ nix-env -u gcc-3.3.2 --always
+$ nix-env --upgrade gcc-3.3.2 --always
 upgrading `gcc-3.4' to `gcc-3.3.2'
 ```
 
@@ -98,7 +98,7 @@ To try to upgrade everything
 (matching packages based on the part of the derivation name without version):
 
 ```console
-$ nix-env -u
+$ nix-env --upgrade
 upgrading `hello-2.1.2' to `hello-2.1.3'
 upgrading `mozilla-1.2' to `mozilla-1.4'
 ```
diff --git a/doc/manual/src/command-ref/nix-instantiate.md b/doc/manual/src/command-ref/nix-instantiate.md
index e55fb2afd..e1b4a3e80 100644
--- a/doc/manual/src/command-ref/nix-instantiate.md
+++ b/doc/manual/src/command-ref/nix-instantiate.md
@@ -88,7 +88,7 @@ Instantiate [store derivation]s from a Nix expression, and build them using `nix
 $ nix-instantiate test.nix (instantiate)
 /nix/store/cigxbmvy6dzix98dxxh9b6shg7ar5bvs-perl-BerkeleyDB-0.26.drv
 
-$ nix-store -r $(nix-instantiate test.nix) (build)
+$ nix-store --realise $(nix-instantiate test.nix) (build)
 ...
 /nix/store/qhqk4n8ci095g3sdp93x7rgwyh9rdvgk-perl-BerkeleyDB-0.26 (output path)
 
@@ -100,30 +100,30 @@ dr-xr-xr-x    2 eelco    users        4096 1970-01-01 01:00 lib
 You can also give a Nix expression on the command line:
 
 ```console
-$ nix-instantiate -E 'with import <nixpkgs> { }; hello'
+$ nix-instantiate --expr 'with import <nixpkgs> { }; hello'
 /nix/store/j8s4zyv75a724q38cb0r87rlczaiag4y-hello-2.8.drv
 ```
 
 This is equivalent to:
 
 ```console
-$ nix-instantiate '<nixpkgs>' -A hello
+$ nix-instantiate '<nixpkgs>' --attr hello
 ```
 
 Parsing and evaluating Nix expressions:
 
 ```console
-$ nix-instantiate --parse -E '1 + 2'
+$ nix-instantiate --parse --expr '1 + 2'
 1 + 2
 ```
 
 ```console
-$ nix-instantiate --eval -E '1 + 2'
+$ nix-instantiate --eval --expr '1 + 2'
 3
 ```
 
 ```console
-$ nix-instantiate --eval --xml -E '1 + 2'
+$ nix-instantiate --eval --xml --expr '1 + 2'
 <?xml version='1.0' encoding='utf-8'?>
 <expr>
   <int value="3" />
@@ -133,7 +133,7 @@ $ nix-instantiate --eval --xml -E '1 + 2'
 The difference between non-strict and strict evaluation:
 
 ```console
-$ nix-instantiate --eval --xml -E 'rec { x = "foo"; y = x; }'
+$ nix-instantiate --eval --xml --expr 'rec { x = "foo"; y = x; }'
 ...
   <attr name="x">
     <string value="foo" />
@@ -148,7 +148,7 @@ Note that `y` is left unevaluated (the XML representation doesn’t
 attempt to show non-normal forms).
 
 ```console
-$ nix-instantiate --eval --xml --strict -E 'rec { x = "foo"; y = x; }'
+$ nix-instantiate --eval --xml --strict --expr 'rec { x = "foo"; y = x; }'
 ...
   <attr name="x">
     <string value="foo" />
diff --git a/doc/manual/src/command-ref/nix-shell.md b/doc/manual/src/command-ref/nix-shell.md
index 576e5ba0b..195b72be5 100644
--- a/doc/manual/src/command-ref/nix-shell.md
+++ b/doc/manual/src/command-ref/nix-shell.md
@@ -89,7 +89,7 @@ All options not listed here are passed to `nix-store
   - `--packages` / `-p` *packages*…\
     Set up an environment in which the specified packages are present.
     The command line arguments are interpreted as attribute names inside
-    the Nix Packages collection. Thus, `nix-shell -p libjpeg openjdk`
+    the Nix Packages collection. Thus, `nix-shell --packages libjpeg openjdk`
     will start a shell in which the packages denoted by the attribute
     names `libjpeg` and `openjdk` are present.
 
@@ -118,7 +118,7 @@ To build the dependencies of the package Pan, and start an interactive
 shell in which to build it:
 
 ```console
-$ nix-shell '<nixpkgs>' -A pan
+$ nix-shell '<nixpkgs>' --attr pan
 [nix-shell]$ eval ${unpackPhase:-unpackPhase}
 [nix-shell]$ cd $sourceRoot
 [nix-shell]$ eval ${patchPhase:-patchPhase}
@@ -137,7 +137,7 @@ To clear the environment first, and do some additional automatic
 initialisation of the interactive shell:
 
 ```console
-$ nix-shell '<nixpkgs>' -A pan --pure \
+$ nix-shell '<nixpkgs>' --attr pan --pure \
     --command 'export NIX_DEBUG=1; export NIX_CORES=8; return'
 ```
 
@@ -146,13 +146,13 @@ Nix expressions can also be given on the command line using the `-E` and
 packages `sqlite` and `libX11`:
 
 ```console
-$ nix-shell -E 'with import <nixpkgs> { }; runCommand "dummy" { buildInputs = [ sqlite xorg.libX11 ]; } ""'
+$ nix-shell --expr 'with import <nixpkgs> { }; runCommand "dummy" { buildInputs = [ sqlite xorg.libX11 ]; } ""'
 ```
 
 A shorter way to do the same is:
 
 ```console
-$ nix-shell -p sqlite xorg.libX11
+$ nix-shell --packages sqlite xorg.libX11
 [nix-shell]$ echo $NIX_LDFLAGS
 … -L/nix/store/j1zg5v…-sqlite-3.8.0.2/lib -L/nix/store/0gmcz9…-libX11-1.6.1/lib …
 ```
@@ -162,7 +162,7 @@ the `buildInputs = [ ... ]` shown above, not only package names. So the
 following is also legal:
 
 ```console
-$ nix-shell -p sqlite 'git.override { withManual = false; }'
+$ nix-shell --packages sqlite 'git.override { withManual = false; }'
 ```
 
 The `-p` flag looks up Nixpkgs in the Nix search path. You can override
@@ -171,7 +171,7 @@ gives you a shell containing the Pan package from a specific revision of
 Nixpkgs:
 
 ```console
-$ nix-shell -p pan -I nixpkgs=https://github.com/NixOS/nixpkgs/archive/8a3eea054838b55aca962c3fbde9c83c102b8bf2.tar.gz
+$ nix-shell --packages pan -I nixpkgs=https://github.com/NixOS/nixpkgs/archive/8a3eea054838b55aca962c3fbde9c83c102b8bf2.tar.gz
 
 [nix-shell:~]$ pan --version
 Pan 0.139
@@ -185,7 +185,7 @@ done by starting the script with the following lines:
 
 ```bash
 #! /usr/bin/env nix-shell
-#! nix-shell -i real-interpreter -p packages
+#! nix-shell -i real-interpreter --packages packages
 ```
 
 where *real-interpreter* is the “real” script interpreter that will be
@@ -202,7 +202,7 @@ For example, here is a Python script that depends on Python and the
 
 ```python
 #! /usr/bin/env nix-shell
-#! nix-shell -i python -p python pythonPackages.prettytable
+#! nix-shell -i python --packages python pythonPackages.prettytable
 
 import prettytable
 
@@ -217,7 +217,7 @@ requires Perl and the `HTML::TokeParser::Simple` and `LWP` packages:
 
 ```perl
 #! /usr/bin/env nix-shell
-#! nix-shell -i perl -p perl perlPackages.HTMLTokeParserSimple perlPackages.LWP
+#! nix-shell -i perl --packages perl perlPackages.HTMLTokeParserSimple perlPackages.LWP
 
 use HTML::TokeParser::Simple;
 
@@ -235,7 +235,7 @@ package like Terraform:
 
 ```bash
 #! /usr/bin/env nix-shell
-#! nix-shell -i bash -p "terraform.withPlugins (plugins: [ plugins.openstack ])"
+#! nix-shell -i bash --packages "terraform.withPlugins (plugins: [ plugins.openstack ])"
 
 terraform apply
 ```
@@ -251,7 +251,7 @@ branch):
 
 ```haskell
 #! /usr/bin/env nix-shell
-#! nix-shell -i runghc -p "haskellPackages.ghcWithPackages (ps: [ps.download-curl ps.tagsoup])"
+#! nix-shell -i runghc --packages "haskellPackages.ghcWithPackages (ps: [ps.download-curl ps.tagsoup])"
 #! nix-shell -I nixpkgs=https://github.com/NixOS/nixpkgs/archive/nixos-20.03.tar.gz
 
 import Network.Curl.Download
diff --git a/doc/manual/src/command-ref/nix-store/dump.md b/doc/manual/src/command-ref/nix-store/dump.md
index 62656d599..c2f3c42ef 100644
--- a/doc/manual/src/command-ref/nix-store/dump.md
+++ b/doc/manual/src/command-ref/nix-store/dump.md
@@ -23,7 +23,7 @@ produce the same NAR archive. For instance, directory entries are
 always sorted so that the actual on-disk order doesn’t influence the
 result.  This means that the cryptographic hash of a NAR dump of a
 path is usable as a fingerprint of the contents of the path. Indeed,
-the hashes of store paths stored in Nix’s database (see `nix-store -q
+the hashes of store paths stored in Nix’s database (see `nix-store --query
 --hash`) are SHA-256 hashes of the NAR dump of each store path.
 
 NAR archives support filenames of unlimited length and 64-bit file
diff --git a/doc/manual/src/command-ref/nix-store/export.md b/doc/manual/src/command-ref/nix-store/export.md
index aeea38636..1bc46f53b 100644
--- a/doc/manual/src/command-ref/nix-store/export.md
+++ b/doc/manual/src/command-ref/nix-store/export.md
@@ -31,7 +31,7 @@ To copy a whole closure, do something
 like:
 
 ```console
-$ nix-store --export $(nix-store -qR paths) > out
+$ nix-store --export $(nix-store --query --requisites paths) > out
 ```
 
 To import the whole closure again, run:
diff --git a/doc/manual/src/command-ref/nix-store/opt-common.md b/doc/manual/src/command-ref/nix-store/opt-common.md
index bf6566555..dd9a6bf21 100644
--- a/doc/manual/src/command-ref/nix-store/opt-common.md
+++ b/doc/manual/src/command-ref/nix-store/opt-common.md
@@ -11,7 +11,7 @@ The following options are allowed for all `nix-store` operations, but may not al
   be created in `/nix/var/nix/gcroots/auto/`. For instance,
 
   ```console
-  $ nix-store --add-root /home/eelco/bla/result -r ...
+  $ nix-store --add-root /home/eelco/bla/result --realise ...
 
   $ ls -l /nix/var/nix/gcroots/auto
   lrwxrwxrwx    1 ... 2005-03-13 21:10 dn54lcypm8f8... -> /home/eelco/bla/result
diff --git a/doc/manual/src/command-ref/nix-store/query.md b/doc/manual/src/command-ref/nix-store/query.md
index 9f7dbd3e8..cd45a4932 100644
--- a/doc/manual/src/command-ref/nix-store/query.md
+++ b/doc/manual/src/command-ref/nix-store/query.md
@@ -145,7 +145,7 @@ Print the closure (runtime dependencies) of the `svn` program in the
 current user environment:
 
 ```console
-$ nix-store -qR $(which svn)
+$ nix-store --query --requisites $(which svn)
 /nix/store/5mbglq5ldqld8sj57273aljwkfvj22mc-subversion-1.1.4
 /nix/store/9lz9yc6zgmc0vlqmn2ipcpkjlmbi51vv-glibc-2.3.4
 ...
@@ -154,7 +154,7 @@ $ nix-store -qR $(which svn)
 Print the build-time dependencies of `svn`:
 
 ```console
-$ nix-store -qR $(nix-store -qd $(which svn))
+$ nix-store --query --requisites $(nix-store --query --deriver $(which svn))
 /nix/store/02iizgn86m42q905rddvg4ja975bk2i4-grep-2.5.1.tar.bz2.drv
 /nix/store/07a2bzxmzwz5hp58nf03pahrv2ygwgs3-gcc-wrapper.sh
 /nix/store/0ma7c9wsbaxahwwl04gbw3fcd806ski4-glibc-2.3.4.drv
@@ -168,7 +168,7 @@ the derivation (`-qd`), not the closure of the output path that contains
 Show the build-time dependencies as a tree:
 
 ```console
-$ nix-store -q --tree $(nix-store -qd $(which svn))
+$ nix-store --query --tree $(nix-store --query --deriver $(which svn))
 /nix/store/7i5082kfb6yjbqdbiwdhhza0am2xvh6c-subversion-1.1.4.drv
 +---/nix/store/d8afh10z72n8l1cr5w42366abiblgn54-builder.sh
 +---/nix/store/fmzxmpjx2lh849ph0l36snfj9zdibw67-bash-3.0.drv
@@ -180,7 +180,7 @@ $ nix-store -q --tree $(nix-store -qd $(which svn))
 Show all paths that depend on the same OpenSSL library as `svn`:
 
 ```console
-$ nix-store -q --referrers $(nix-store -q --binding openssl $(nix-store -qd $(which svn)))
+$ nix-store --query --referrers $(nix-store --query --binding openssl $(nix-store --query --deriver $(which svn)))
 /nix/store/23ny9l9wixx21632y2wi4p585qhva1q8-sylpheed-1.0.0
 /nix/store/5mbglq5ldqld8sj57273aljwkfvj22mc-subversion-1.1.4
 /nix/store/dpmvp969yhdqs7lm2r1a3gng7pyq6vy4-subversion-1.1.3
@@ -191,7 +191,7 @@ Show all paths that directly or indirectly depend on the Glibc (C
 library) used by `svn`:
 
 ```console
-$ nix-store -q --referrers-closure $(ldd $(which svn) | grep /libc.so | awk '{print $3}')
+$ nix-store --query --referrers-closure $(ldd $(which svn) | grep /libc.so | awk '{print $3}')
 /nix/store/034a6h4vpz9kds5r6kzb9lhh81mscw43-libgnomeprintui-2.8.2
 /nix/store/15l3yi0d45prm7a82pcrknxdh6nzmxza-gawk-3.1.4
 ...
@@ -204,7 +204,7 @@ Make a picture of the runtime dependency graph of the current user
 environment:
 
 ```console
-$ nix-store -q --graph ~/.nix-profile | dot -Tps > graph.ps
+$ nix-store --query --graph ~/.nix-profile | dot -Tps > graph.ps
 $ gv graph.ps
 ```
 
@@ -212,7 +212,7 @@ Show every garbage collector root that points to a store path that
 depends on `svn`:
 
 ```console
-$ nix-store -q --roots $(which svn)
+$ nix-store --query --roots $(which svn)
 /nix/var/nix/profiles/default-81-link
 /nix/var/nix/profiles/default-82-link
 /home/eelco/.local/state/nix/profiles/profile-97-link
diff --git a/doc/manual/src/command-ref/nix-store/read-log.md b/doc/manual/src/command-ref/nix-store/read-log.md
index 4a88e9382..d1ff17891 100644
--- a/doc/manual/src/command-ref/nix-store/read-log.md
+++ b/doc/manual/src/command-ref/nix-store/read-log.md
@@ -27,7 +27,7 @@ substitute, then the log is unavailable.
 # Example
 
 ```console
-$ nix-store -l $(which ktorrent)
+$ nix-store --read-log $(which ktorrent)
 building /nix/store/dhc73pvzpnzxhdgpimsd9sw39di66ph1-ktorrent-2.2.1
 unpacking sources
 unpacking source archive /nix/store/p8n1jpqs27mgkjw07pb5269717nzf5f8-ktorrent-2.2.1.tar.gz
diff --git a/doc/manual/src/command-ref/nix-store/realise.md b/doc/manual/src/command-ref/nix-store/realise.md
index f61a20100..6b50d2145 100644
--- a/doc/manual/src/command-ref/nix-store/realise.md
+++ b/doc/manual/src/command-ref/nix-store/realise.md
@@ -99,7 +99,7 @@ This operation is typically used to build [store derivation]s produced by
 [store derivation]: @docroot@/glossary.md#gloss-store-derivation
 
 ```console
-$ nix-store -r $(nix-instantiate ./test.nix)
+$ nix-store --realise $(nix-instantiate ./test.nix)
 /nix/store/31axcgrlbfsxzmfff1gyj1bf62hvkby2-aterm-2.3.1
 ```
 
@@ -108,7 +108,7 @@ This is essentially what [`nix-build`](@docroot@/command-ref/nix-build.md) does.
 To test whether a previously-built derivation is deterministic:
 
 ```console
-$ nix-build '<nixpkgs>' -A hello --check -K
+$ nix-build '<nixpkgs>' --attr hello --check -K
 ```
 
 Use [`nix-store --read-log`](./read-log.md) to show the stderr and stdout of a build:
diff --git a/doc/manual/src/command-ref/nix-store/verify-path.md b/doc/manual/src/command-ref/nix-store/verify-path.md
index 59ffe92a3..927201599 100644
--- a/doc/manual/src/command-ref/nix-store/verify-path.md
+++ b/doc/manual/src/command-ref/nix-store/verify-path.md
@@ -24,6 +24,6 @@ path has changed, and 1 otherwise.
 To verify the integrity of the `svn` command and all its dependencies:
 
 ```console
-$ nix-store --verify-path $(nix-store -qR $(which svn))
+$ nix-store --verify-path $(nix-store --query --requisites $(which svn))
 ```
 
diff --git a/doc/manual/src/command-ref/opt-common.md b/doc/manual/src/command-ref/opt-common.md
index 7a012250d..54c0a1d0d 100644
--- a/doc/manual/src/command-ref/opt-common.md
+++ b/doc/manual/src/command-ref/opt-common.md
@@ -162,11 +162,11 @@ Most Nix commands accept the following command-line options:
     }: ...
     ```
 
-    So if you call this Nix expression (e.g., when you do `nix-env -iA
+    So if you call this Nix expression (e.g., when you do `nix-env --install --attr
     pkgname`), the function will be called automatically using the
     value [`builtins.currentSystem`](@docroot@/language/builtins.md) for
     the `system` argument. You can override this using `--arg`, e.g.,
-    `nix-env -iA pkgname --arg system \"i686-freebsd\"`. (Note that
+    `nix-env --install --attr pkgname --arg system \"i686-freebsd\"`. (Note that
     since the argument is a Nix string literal, you have to escape the
     quotes.)
 
@@ -199,7 +199,7 @@ Most Nix commands accept the following command-line options:
     For `nix-shell`, this option is commonly used to give you a shell in
     which you can build the packages returned by the expression. If you
     want to get a shell which contain the *built* packages ready for
-    use, give your expression to the `nix-shell -p` convenience flag
+    use, give your expression to the `nix-shell --packages ` convenience flag
     instead.
 
   - <span id="opt-I">[`-I`](#opt-I)</span> *path*\