Split nix-env and nix-store documentation per-subcommand

Documentation on "classic" commands with many sub-commands are
notoriously hard to discover due to lack of overview and anchor links.
Additionally the information on common options and environment variables
is not accessible offline in man pages, and therefore often overlooked
by readers.

With this change, each sub-command of nix-store and nix-env gets its
own page in the manual (listed in the table of contents), and each own
man page.

Also, man pages for each subcommand now (again) list common options
and environment variables. While this makes each page quite long and
some common parameters don't apply, this should still make it easier
to navigate as that additional information was not accessible on the
command line at all.

It is now possible to run 'nix-store --<subcommand> --help` to display
help pages for the given subcommand.

Co-authored-by: Valentin Gagarin <valentin.gagarin@tweag.io>

doc/manual/src/command-ref/nix-env/upgrade.md

@@ -0,0 +1,141 @@
+# Name
+
+`nix-env --upgrade` - upgrade packages in user environment
+
+# Synopsis
+
+`nix-env` {`--upgrade` | `-u`} *args*
+  [`--lt` | `--leq` | `--eq` | `--always`]
+  [{`--prebuilt-only` | `-b`}]
+  [{`--attr` | `-A`}]
+  [`--from-expression`] [`-E`]
+  [`--from-profile` *path*]
+  [`--preserve-installed` | `-P`]
+
+# Description
+
+The upgrade operation creates a new user environment, based on the
+current generation of the active profile, in which all store paths are
+replaced for which there are newer versions in the set of paths
+described by *args*. Paths for which there are no newer versions are
+left untouched; this is not an error. It is also not an error if an
+element of *args* matches no installed derivations.
+
+For a description of how *args* is mapped to a set of store paths, see
+[`--install`](#operation---install). If *args* describes multiple
+store paths with the same symbolic name, only the one with the highest
+version is installed.
+
+# Flags
+
+  - `--lt`\
+    Only upgrade a derivation to newer versions. This is the default.
+
+  - `--leq`\
+    In addition to upgrading to newer versions, also “upgrade” to
+    derivations that have the same version. Version are not a unique
+    identification of a derivation, so there may be many derivations
+    that have the same version. This flag may be useful to force
+    “synchronisation” between the installed and available derivations.
+
+  - `--eq`\
+    *Only* “upgrade” to derivations that have the same version. This may
+    not seem very useful, but it actually is, e.g., when there is a new
+    release of Nixpkgs and you want to replace installed applications
+    with the same versions built against newer dependencies (to reduce
+    the number of dependencies floating around on your system).
+
+  - `--always`\
+    In addition to upgrading to newer versions, also “upgrade” to
+    derivations that have the same or a lower version. I.e., derivations
+    may actually be downgraded depending on what is available in the
+    active Nix expression.
+
+  - `--prebuilt-only` / `-b`\
+    Use only derivations for which a substitute is registered, i.e.,
+    there is a pre-built binary available that can be downloaded in lieu
+    of building the derivation. Thus, no packages will be built from
+    source.
+
+  - `--preserve-installed` / `-P`\
+    Do not remove derivations with a name matching one of the
+    derivations being installed. Usually, trying to have two versions of
+    the same package installed in the same generation of a profile will
+    lead to an error in building the generation, due to file name
+    clashes between the two versions. However, this is not the case for
+    all packages.
+
+{{#include ./opt-common.md}}
+
+{{#include ../opt-common.md}}
+
+{{#include ./env-common.md}}
+
+{{#include ../env-common.md}}
+
+# Examples
+
+```console
+$ nix-env --upgrade -A 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
+```
+
+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
+upgrading `gcc-3.4' to `gcc-3.3.2'
+```
+
+To try to upgrade everything
+(matching packages based on the part of the derivation name without version):
+
+```console
+$ nix-env -u
+upgrading `hello-2.1.2' to `hello-2.1.3'
+upgrading `mozilla-1.2' to `mozilla-1.4'
+```
+
+# Versions
+
+The upgrade operation determines whether a derivation `y` is an upgrade
+of a derivation `x` by looking at their respective `name` attributes.
+The names (e.g., `gcc-3.3.1` are split into two parts: the package name
+(`gcc`), and the version (`3.3.1`). The version part starts after the
+first dash not followed by a letter. `y` is considered an upgrade of `x`
+if their package names match, and the version of `y` is higher than that
+of `x`.
+
+The versions are compared by splitting them into contiguous components
+of numbers and letters. E.g., `3.3.1pre5` is split into `[3, 3, 1,
+"pre", 5]`. These lists are then compared lexicographically (from left
+to right). Corresponding components `a` and `b` are compared as follows.
+If they are both numbers, integer comparison is used. If `a` is an empty
+string and `b` is a number, `a` is considered less than `b`. The special
+string component `pre` (for *pre-release*) is considered to be less than
+other components. String components are considered less than number
+components. Otherwise, they are compared lexicographically (i.e., using
+case-sensitive string comparison).
+
+This is illustrated by the following examples:
+
+    1.0 < 2.3
+    2.1 < 2.3
+    2.3 = 2.3
+    2.5 > 2.3
+    3.1 > 2.3
+    2.3.1 > 2.3
+    2.3.1 > 2.3a
+    2.3pre1 < 2.3
+    2.3pre3 < 2.3pre12
+    2.3a < 2.3c
+    2.3pre1 < 2.3c
+    2.3pre1 < 2.3q
+