docs: retire the agent hierarchy from every page that described it

The topology doc keeps its filename and its second half (manager
special-casing, harness unit shape) — both are cross-referenced from
other pages and neither is about the parent field. Its first half is
rewritten: what topology.json is now, and a table of what the removal
took with it, so a reader who finds `<parent>` or `set-parent` in an old
issue thread learns it went away rather than moved.

The dashboard's tree-rendering section is marked dormant rather than
deleted: the walk is still in swarm.js and retiring it is the frontend
owner's call.

frontend/packages/dashboard/src/swarm.js

@@ -952,7 +952,6 @@ export function renderSelectionBar(containers) {
     confirm: (names) =>
       `PURGE ${names.length} agent${names.length === 1 ? "" : "s"} (${names.join(", ")})? containers, config history, claude creds, and notes are all WIPED. no undo.`,
   });
-
 }
 
 function addBulkButton(parent, btnClass, label, enabled, selected, opts) {