docs+comments: say what changed instead of tagging the tracker item

The prose added by this branch named the tracker item in seventeen
places, which check-issue-refs.sh rejects: a `#N` tag is dead weight for
anyone reading the public mirror, where no issue data exists. Each one
now states the fact it was pointing at — the parent field is gone — so
the sentence stands on its own.

Two of those lines also carried a rustdoc break: `[`write`]` in
topology.rs is ambiguous between the module's own `write` fn and the
`write!` macro, which `-D rustdoc::broken-intra-doc-links` fails. Spelled
`[`write()`]`, per rustdoc's own suggestion.

The host_config.rs rewrite is two lines rather than three so the doc
block stays under check-comment-blocks.sh's 30-line ceiling.

docs/agent-lifecycle/agent-hierarchy.md

@@ -2,8 +2,8 @@
 
 <!-- vale write-good.Passive = NO -->
 
-Agents are a **flat set**, with no parent/child tree: #4472 removed the
-`parent` field `topology.json` used to carry, and every mechanism that
+Agents are a **flat set**, with no parent/child tree: the `parent` field
+`topology.json` used to carry is gone, along with every mechanism that
 read it. The capability store scopes which agents can manage which
 others; a tree position no longer scopes anything.
 
@@ -33,7 +33,7 @@ agent's `state` read-write and `config` read-only; never `harness`). An
 agent holding no capability sees its own dirs and nothing else. See
 [`persistence.md`](persistence.md)'s _Cross-agent access to state._
 
-### Reading the pre-#4472 format
+### Reading the legacy format
 
 `topology.json` used to be a map of `name → parent | null`. The reader
 still accepts that shape and keeps its keys, so a hive upgrading across