diff --git a/doc/manual/source/command-ref/nix-store/query.md b/doc/manual/source/command-ref/nix-store/query.md
index 601f46af6b2..b5ba63adae2 100644
--- a/doc/manual/source/command-ref/nix-store/query.md
+++ b/doc/manual/source/command-ref/nix-store/query.md
@@ -45,10 +45,19 @@ symlink.
 
   [output paths]: @docroot@/glossary.md#gloss-output-path
 
+- `--references`
+
+  Prints the set of [references] of the store paths
+  *paths*, that is, their immediate dependencies. (For *all*
+  dependencies, use `--requisites`.)
+
+  [references]: @docroot@/glossary.md#gloss-reference
+
 - `--requisites` / `-R`
 
-  Prints out the [closure] of the store path *paths*.
+  Prints out the set of [*requisites*][requisite] (better known as the [closure]) of the store path *paths*.
 
+  [requisite]: @docroot@/glossary.md#gloss-requisite
   [closure]: @docroot@/glossary.md#gloss-closure
 
   This query has one option:
@@ -65,29 +74,25 @@ symlink.
   dependencies) is obtained by distributing the closure of a store
   derivation and specifying the option `--include-outputs`.
 
-- `--references`
-
-  Prints the set of [references] of the store paths
-  *paths*, that is, their immediate dependencies. (For *all*
-  dependencies, use `--requisites`.)
-
-  [references]: @docroot@/glossary.md#gloss-reference
-
 - `--referrers`
 
-  Prints the set of *referrers* of the store paths *paths*, that is,
+  Prints the set of [*referrers*][referrer] of the store paths *paths*, that is,
   the store paths currently existing in the Nix store that refer to
   one of *paths*. Note that contrary to the references, the set of
   referrers is not constant; it can change as store paths are added or
   removed.
 
+  [referrer]: @docroot@/glossary.md#gloss-referrer
+
 - `--referrers-closure`
 
   Prints the closure of the set of store paths *paths* under the
-  referrers relation; that is, all store paths that directly or
+  [referrers relation][referrer]; that is, all store paths that directly or
   indirectly refer to one of *paths*. These are all the path currently
   in the Nix store that are dependent on *paths*.
 
+  [referrer]: @docroot@/glossary.md#gloss-referrer
+
 - `--deriver` / `-d`
 
   Prints the [deriver] that was used to build the store paths *paths*. If
diff --git a/doc/manual/source/development/contributing.md b/doc/manual/source/development/contributing.md
index 7de7489dcb7..5c32aeb712a 100644
--- a/doc/manual/source/development/contributing.md
+++ b/doc/manual/source/development/contributing.md
@@ -20,8 +20,9 @@ prs: 1238
 Here's one or more paragraphs that describe the change.
 
 - It's markdown
-- Add references to the manual using @docroot@
+- Add references to the manual using [links like this](@_at_docroot@/example.md)
 ```
+<!-- for the raw markdown readers: that means using @docroot@ -->
 
 Significant changes should add the following header, which moves them to the top.
 
diff --git a/doc/manual/source/glossary.md b/doc/manual/source/glossary.md
index f38664a0265..37b1ff6ec59 100644
--- a/doc/manual/source/glossary.md
+++ b/doc/manual/source/glossary.md
@@ -38,6 +38,13 @@
 
   [store derivation]: #gloss-store-derivation
 
+- [directed acyclic graph]{#gloss-directed-acyclic-graph}
+
+  A [directed acyclic graph](https://en.wikipedia.org/wiki/Directed_acyclic_graph) (DAG) is graph whose edges are given a direction ("a to b" is not the same edge as "b to a"), and for which no possible path (created by joining together edges) forms a cycle.
+
+  DAGs are very important to Nix.
+  In particular, the non-self-[references][reference] of [store object][store object] form a cycle.
+
 - [derivation path]{#gloss-derivation-path}
 
   A [store path] which uniquely identifies a [store derivation].
@@ -156,6 +163,8 @@
   non-[fixed-output](#gloss-fixed-output-derivation)
   derivation.
 
+  See [input-addressing derivation outputs](store/derivation/outputs/input-address.md) for details.
+
 - [content-addressed store object]{#gloss-content-addressed-store-object}
 
   A [store object] which is [content-addressed](#gloss-content-address),
@@ -219,19 +228,21 @@
 
 - [reference]{#gloss-reference}
 
-  A [store object] `O` is said to have a *reference* to a store object `P` if a [store path] to `P` appears in the contents of `O`.
+  An edge from one [store object] to another.
 
-  Store objects can refer to both other store objects and themselves.
-  References from a store object to itself are called *self-references*.
-  References other than a self-reference must not form a cycle.
+  See [References](@docroot@/store/store-object.md#references) for details.
 
   [reference]: #gloss-reference
 
+  See [References](@docroot@/store/store-object.md#references) for details.
+
 - [reachable]{#gloss-reachable}
 
   A store path `Q` is reachable from another store path `P` if `Q`
   is in the *closure* of the *references* relation.
 
+  See [References](@docroot@/store/store-object.md#references) for details.
+
 - [closure]{#gloss-closure}
 
   The closure of a store path is the set of store paths that are
@@ -248,8 +259,21 @@
   to a store object at path `Q`, then `Q` is in the closure of `P`. Further, if `Q`
   references `R` then `R` is also in the closure of `P`.
 
+  See [References](@docroot@/store/store-object.md#references) for details.
+
   [closure]: #gloss-closure
 
+- [requisite]{#gloss-requisite}
+
+  A store object [reachable] by a path (chain of references) from a given [store object].
+  The [closure] is the set of requisites.
+
+  See [References](@docroot@/store/store-object.md#references) for details.
+
+- [referrer]{#gloss-reference}
+
+  A reversed edge from one [store object] to another.
+
 - [output]{#gloss-output}
 
   A [store object] produced by a [store derivation].
diff --git a/doc/manual/source/language/advanced-attributes.md b/doc/manual/source/language/advanced-attributes.md
index 4af255bf34e..a939847e1aa 100644
--- a/doc/manual/source/language/advanced-attributes.md
+++ b/doc/manual/source/language/advanced-attributes.md
@@ -79,6 +79,8 @@ Derivations can declare some infrequently used optional attributes.
 
 ## Output checks
 
+See the [corresponding section in the derivation output page](@docroot@/store/derivation/outputs/index.md).
+
   - [`allowedReferences`]{#adv-attr-allowedReferences}\
     The optional attribute `allowedReferences` specifies a list of legal
     references (dependencies) of the output of the builder. For example,
diff --git a/doc/manual/source/language/operators.md b/doc/manual/source/language/operators.md
index dbf2441cb7c..ab74e8a9999 100644
--- a/doc/manual/source/language/operators.md
+++ b/doc/manual/source/language/operators.md
@@ -196,7 +196,7 @@ All comparison operators are implemented in terms of `<`, and the following equi
 
 ## Logical implication
 
-Equivalent to `!`*b1* `||` *b2*.
+Equivalent to `!`*b1* `||` *b2*  (or `if` *b1* `then` *b2* `else true`)
 
 [Logical implication]: #logical-implication
 
diff --git a/doc/manual/source/store/store-object.md b/doc/manual/source/store/store-object.md
index caf5657d1f0..660d02f2a57 100644
--- a/doc/manual/source/store/store-object.md
+++ b/doc/manual/source/store/store-object.md
@@ -4,7 +4,64 @@ A Nix store is a collection of *store objects* with *references* between them.
 A store object consists of
 
   - A [file system object](./file-system-object.md) as data
-  - A set of [store paths](./store-path.md) as references to other store objects
+
+  - A set of [store paths](./store-path.md) as references to store objects
+
+### References
+
+Store objects can refer to both other store objects and themselves.
+References from a store object to itself are called *self-references*.
+
+Store objects and their references form a directed graph, where the store objects are the vertices, and the references are the edges.
+In particular, the edge corresponding to a reference is from the store object that contains the reference, and to the store object that the store path (which is the reference) refers to.
+
+References other than a self-reference must not form a cycle.
+The graph of references excluding self-references thus forms a [directed acyclic graph].
+
+[directed acyclic graph]: @docroot@/glossary.md#gloss-directed acyclic graph
+
+We can take the [transitive closure] of the references graph, which any pair of store objects have an edge not if there is a single reference from the first to the second, but a path of one or more references from the first to the second.
+The *requisites* of a store object are all store objects reachable by paths of references which start with given store object's references.
+
+[transitive closure]: https://en.wikipedia.org/wiki/Transitive_closure
+
+We can also take the [transpose graph] ofthe references graph, where we reverse the orientation of all edges.
+The *referrers* of a store object are the store objects that reference it.
+
+[transpose graph]: https://en.wikipedia.org/wiki/Transpose_graph
+
+One can also combine both concepts: taking the transitive closure of the tranposed references graph.
+The *referrers closure* of a store object are the store objects that can reach the given store object via paths of references.
+
+> **Note**
+>
+> Care must be taken to distinguish between the intrinsic and extrinsic properties of store objects.
+> We can create graphs from the store objects in a store, but the contents of the store is not, in general fixed, and may instead change over time.
+>
+> - The references of a store object --- the set of store paths called the references --- is a field of a store object, and thus intrinsic by definition.
+    Regardless of what store contains the store object in question, and what else that store may or may not contain, the references are the same.
+>
+> - The requisites of a store object are almost intrinsic --- some store paths due not precisely refer to a unique single store object.
+> Exactly what store object is being referenced, and what in turn *its* references are, depends on the store in question.
+>   Different stores that disagree.
+>
+> - The referrers of a store object are completely extrinsic, and depends solely on the store which contains that store object, not the store object itself.
+>   Other store objects which refer to the store object in question may be added or removed from the store.
+
+### Immutability
 
 Store objects are [immutable](https://en.wikipedia.org/wiki/Immutable_object):
-Once created, they do not change until they are deleted.
+Once created, they do not change nor can any store object they reference be changed.
+
+> **Note**
+>
+> Stores which support atomically deleting multiple store objects allow more flexibility while still upholding this property.
+
+### Closure property
+
+A store can only contain a store object if it also contains all the store objects it refers to.
+
+> **Note**
+>
+> The "closure property" isn't meant to prohibit, for example, [lazy loading](https://en.wikipedia.org/wiki/Lazy_loading) of store objects.
+> However, the "closure property" and immutability in conjunction imply that any such lazy loading ought to be deterministic.
diff --git a/doc/manual/substitute.py b/doc/manual/substitute.py
index a8b11d93250..6e27c338818 100644
--- a/doc/manual/substitute.py
+++ b/doc/manual/substitute.py
@@ -57,6 +57,9 @@ def recursive_replace(data: dict[str, t.Any], book_root: Path, search_path: Path
                     ).replace(
                         '@docroot@',
                         ("../" * len(path_to_chapter.parent.parts) or "./")[:-1]
+                    ).replace(
+                        '@_at_',
+                        '@'
                     ),
                     sub_items = [
                         recursive_replace(sub_item, book_root, search_path)
diff --git a/docker.nix b/docker.nix
index d52c317d6b1..2670f8394ca 100644
--- a/docker.nix
+++ b/docker.nix
@@ -173,7 +173,12 @@ let
       channel = pkgs.runCommand "channel-nixos" { inherit bundleNixpkgs; } ''
         mkdir $out
         if [ "$bundleNixpkgs" ]; then
-          ln -s ${nixpkgs} $out/nixpkgs
+          ln -s ${
+            builtins.path {
+              path = nixpkgs;
+              name = "source";
+            }
+          } $out/nixpkgs
           echo "[]" > $out/manifest.nix
         fi
       '';
diff --git a/scripts/nix-profile-daemon.fish.in b/scripts/nix-profile-daemon.fish.in
index 2ecab007766..da4c61bc1c6 100644
--- a/scripts/nix-profile-daemon.fish.in
+++ b/scripts/nix-profile-daemon.fish.in
@@ -24,7 +24,33 @@ end
 
 # Set up the per-user profile.
 
-set --local NIX_LINK $HOME/.nix-profile
+set --local NIX_LINK "$HOME/.nix-profile"
+set --local NIX_LINK_NEW
+if test -n "$XDG_STATE_HOME"
+    set NIX_LINK_NEW "$XDG_STATE_HOME/nix/profile"
+else
+    set NIX_LINK_NEW "$HOME/.local/state/nix/profile"
+end
+if test -e "$NIX_LINK_NEW"
+    if test -t 2; and test -e "$NIX_LINK"
+        set --local warning "\033[1;35mwarning:\033[0m "
+        printf "$warning Both %s and legacy %s exist; using the former.\n" "$NIX_LINK_NEW" "$NIX_LINK" 1>&2
+
+        if test (realpath "$NIX_LINK") = (realpath "$NIX_LINK_NEW")
+            printf "         Since the profiles match, you can safely delete either of them.\n" 1>&2
+        else
+            # This should be an exceptionally rare occasion: the only way to get it would be to
+            # 1. Update to newer Nix;
+            # 2. Remove .nix-profile;
+            # 3. Set the $NIX_LINK_NEW to something other than the default user profile;
+            # 4. Roll back to older Nix.
+            # If someone did all that, they can probably figure out how to migrate the profile.
+            printf "$warning Profiles do not match. You should manually migrate from %s to %s.\n" "$NIX_LINK" "$NIX_LINK_NEW" 1>&2
+        end
+    end
+
+    set NIX_LINK "$NIX_LINK_NEW"
+end
 
 # Set up environment.
 # This part should be kept in sync with nixpkgs:nixos/modules/programs/environment.nix
diff --git a/scripts/nix-profile.fish.in b/scripts/nix-profile.fish.in
index 05d9a187de3..b73b92ad127 100644
--- a/scripts/nix-profile.fish.in
+++ b/scripts/nix-profile.fish.in
@@ -24,7 +24,38 @@ end
 
 # Set up the per-user profile.
 
-set --local NIX_LINK $HOME/.nix-profile
+set --local NIX_LINK
+if test -n "$NIX_STATE_HOME"
+    set NIX_LINK "$NIX_STATE_HOME/.nix-profile"
+else
+    set NIX_LINK "$HOME/.nix-profile"
+    set --local NIX_LINK_NEW
+    if test -n "$XDG_STATE_HOME"
+        set NIX_LINK_NEW "$XDG_STATE_HOME/nix/profile"
+    else
+        set NIX_LINK_NEW "$HOME/.local/state/nix/profile"
+    end
+    if test -e "$NIX_LINK_NEW"
+        if test -t 2; and test -e "$NIX_LINK"
+            set --local warning "\033[1;35mwarning:\033[0m "
+            printf "$warning Both %s and legacy %s exist; using the former.\n" "$NIX_LINK_NEW" "$NIX_LINK" 1>&2
+
+            if test (realpath "$NIX_LINK") = (realpath "$NIX_LINK_NEW")
+                printf "         Since the profiles match, you can safely delete either of them.\n" 1>&2
+            else
+                # This should be an exceptionally rare occasion: the only way to get it would be to
+                # 1. Update to newer Nix;
+                # 2. Remove .nix-profile;
+                # 3. Set the $NIX_LINK_NEW to something other than the default user profile;
+                # 4. Roll back to older Nix.
+                # If someone did all that, they can probably figure out how to migrate the profile.
+                printf "$warning Profiles do not match. You should manually migrate from %s to %s.\n" "$NIX_LINK" "$NIX_LINK_NEW" 1>&2
+            end
+        end
+
+        set NIX_LINK "$NIX_LINK_NEW"
+    end
+end
 
 # Set up environment.
 # This part should be kept in sync with nixpkgs:nixos/modules/programs/environment.nix