docs: revise graph docs from review

docs/graph-atlas.md

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+<!-- Generated by scripts/gen-doc-graphs.ts - do not edit by hand.
+     Run `pnpm run gen-doc-graphs` to regenerate. -->
+
+# Documentation Graph Index
+
+Maintenance mode: mixed: each linked page declares generated, hybrid, or curated mode.
+
+These diagrams are the relationship layer above the generated catalogs. Use them to navigate package topology, capability seams, event flow, model-facing tools, app composition, and runtime lifecycle paths. Exact signatures and type shapes still live in [cordis-catalog/](cordis-catalog/events-and-services.md), [tool-catalog/](tool-catalog/tools.md), and [core-data-structures/](core-data-structures/core.md).
+
+The process decision behind this index is recorded in [the documentation graph RFC](rfc/implemented/process/2026-07-03-documentation-graph-atlas.md).
+
+| Graph | Mode |
+| --- | --- |
+| [module dependency graph](module-graph.md) | `generated` |
+| [tool schema catalog and package map](tool-catalog/tools.md) | `generated` |
+| [capability seams and core services](capability-seams.md) | `hybrid generated` |
+| [echo-agent app composition](echo-agent-composition.md) | `hybrid generated` |
+| [coding-agent app composition](coding-agent-composition.md) | `hybrid generated` |
+| [acp-agent app composition](acp-agent-composition.md) | `hybrid generated` |
+| [event producer/consumer matrix](event-producer-consumer.md) | `hybrid generated` |
+| [agent turn and step lifecycle](agent-lifecycle.md) | `curated` |
+| [tool execution pipeline](tool-execution-pipeline.md) | `curated` |
+| [ACP snapshot replay](acp/snapshot-replay.md) | `curated` |
+
+Regenerate with `pnpm run gen-doc-graphs`; verify freshness with `pnpm run verify-doc-graphs`.