Document more references concepts

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

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].
@@ -155,6 +162,8 @@
   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),
@@ -218,19 +227,21 @@
 
 - [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
@@ -247,8 +258,21 @@
   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].

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,

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.