docs: revise graph docs from review

docs/rfc/README.md

@@ -169,7 +169,7 @@ Do NOT write one for a mechanical or local choice (a variable name, a one-file r
 | [Classify RFCs by kind via path-encoded subdirectories](implemented/process/2026-06-20-rfc-classification.md) | 2026-06-20 |
 | [Bilingual documentation via paired sibling files and a pairing gate](implemented/process/2026-07-02-bilingual-docs-and-pairing-gate.md) | 2026-07-02 |
 | [Generated tool-schema catalog (boot-and-harvest)](implemented/process/2026-07-02-tool-schema-catalog.md) | 2026-07-02 |
-| [Documentation graph atlas for maintainers and SDK users](implemented/process/2026-07-03-documentation-graph-atlas.md) | 2026-07-03 |
+| [Documentation graph index for maintainers and SDK users](implemented/process/2026-07-03-documentation-graph-atlas.md) | 2026-07-03 |
 | [JSDoc completeness gate for the cordis surface](implemented/process/2026-07-04-cordis-jsdoc-completeness-gate.md) | 2026-07-04 |
 | [Documentation tiers, budgets, and the ceiling gate](implemented/process/2026-07-04-doc-tiers-and-budgets.md) | 2026-07-04 |
 | [Generate the RFC index tables](implemented/process/2026-07-04-generate-rfc-index-tables.md) | 2026-07-04 |

docs/rfc/implemented/process/2026-07-03-documentation-graph-atlas.md

@@ -1,4 +1,4 @@
-# RFC: Documentation graph atlas for maintainers and SDK users
+# RFC: Documentation graph index for maintainers and SDK users
 
 Status: implemented (accepted 2026-07-03)
 
@@ -12,9 +12,9 @@ The pressure is already visible in the open stacks even though this implementati
 
 ## Decision
 
-Add a generated graph atlas under [docs/graphs/](../../../graphs/README.md), produced by `scripts/gen-doc-graphs.ts` and verified by `pnpm run verify-doc-graphs` as part of `doc-sync`.
+Add generated relationship graph docs, indexed at [docs/graph-atlas.md](../../../graph-atlas.md), produced by focused generators and verified by `pnpm run verify-doc-graphs` / existing catalog freshness checks as part of `doc-sync`.
 
-The atlas is a relationship layer above the existing catalogs. It does not replace exact references; instead, it links to them and explains how their pieces fit together.
+The index is a relationship layer above the existing catalogs. It does not replace exact references; instead, it links to them and explains how their pieces fit together.
 
 ### Maintenance modes
 
@@ -22,36 +22,36 @@ Every graph page declares one maintenance mode:
 
 - **Generated**: all nodes and edges are discovered from source; `--check` fails if the committed artifact is stale.
 - **Hybrid generated**: source discovers the inventory, a small manifest classifies irreducible policy, and a completeness guard fails if discovered items are unclassified.
-- **Curated**: the diagram explains design intent, temporal order, or ownership; it is emitted by the generator so the atlas remains a single regenerated unit, but the content is deliberately authored.
+- **Curated**: the diagram explains design intent, temporal order, or ownership; it is emitted by the generator so the graph docs remain a regenerated unit, but the content is deliberately authored.
 
-### First shipped atlas
+### First shipped index
 
-The first atlas ships twelve files: the index plus eleven graph pages.
+The first index links ten relationship surfaces. Package topology and tool-package affordances live in the existing generated catalogs that already own those facts; the remaining focused diagrams are generated by `scripts/gen-doc-graphs.ts`.
 
 | Graph | Maintenance mode | Source of truth |
 |---|---|---|
-| [package topology by group](../../../graphs/package-topology.md) | generated | `packages/*/*/package.json` peer dependencies plus package group paths |
-| [capability seams and core services](../../../graphs/capability-seams.md) | hybrid generated | Cordis service declarations plus a role manifest in `gen-doc-graphs.ts` |
-| [app composition](../../../graphs/app-composition.md) | hybrid generated | `examples/*/cordis.yml` plugin lists plus curated app/bundle expansions |
-| [event producer/consumer matrix](../../../graphs/event-producer-consumer.md) | hybrid generated | Cordis event declarations, AST-scanned `ctx.on/emit/parallel/serial/waterfall` sites, and explicit dynamic dispatch overrides |
-| [tool affordance map](../../../graphs/tool-affordance-map.md) | hybrid generated | boot-harvested tool catalog plus a manifest of required services and shipped aliases |
-| [agent turn and step lifecycle](../../../graphs/agent-lifecycle.md) | curated | architecture.md loop lifecycle, Cordis catalog links, and session event semantics |
-| [tool execution pipeline](../../../graphs/tool-execution-pipeline.md) | curated | tool pipeline semantics and the `tools/execute` waterfall |
-| [session surface and message projection](../../../graphs/session-surface.md) | curated | session surface/event-sourcing docs |
-| [subagent and session lineage](../../../graphs/subagent-lineage.md) | curated | subagent seam docs and replay/fork semantics |
-| [plugin disposal and hot reload ownership](../../../graphs/hot-reload-disposal.md) | curated | Cordis fiber/effect ownership conventions |
-| [ACP snapshot replay](../../../graphs/snapshot-replay.md) | curated | snapshot harness behavior |
+| [module dependency graph](../../../module-graph.md) | generated | `packages/*/*/package.json` peer dependencies plus package group paths |
+| [tool schema catalog and package map](../../../tool-catalog/tools.md) | generated | boot-harvested tool schemas plus tool-package service/effect metadata |
+| [capability seams and core services](../../../capability-seams.md) | hybrid generated | Cordis service declarations plus a role manifest in `gen-doc-graphs.ts` |
+| [echo-agent app composition](../../../echo-agent-composition.md) | hybrid generated | `examples/echo-agent/cordis.yml` plugin list plus curated app/bundle expansion |
+| [coding-agent app composition](../../../coding-agent-composition.md) | hybrid generated | `examples/coding-agent/cordis.yml` plugin list plus curated app/bundle expansion |
+| [acp-agent app composition](../../../acp-agent-composition.md) | hybrid generated | `examples/acp-agent/cordis.yml` plugin list plus curated app/bundle expansion |
+| [event producer/consumer matrix](../../../event-producer-consumer.md) | hybrid generated | Cordis event declarations, AST-scanned `ctx.on/emit/parallel/serial/waterfall` sites, and explicit dynamic dispatch overrides |
+| [agent turn and step lifecycle](../../../agent-lifecycle.md) | curated | architecture.md loop lifecycle, Cordis catalog links, and session event semantics |
+| [tool execution pipeline](../../../tool-execution-pipeline.md) | curated | tool pipeline semantics and the `tools/execute` waterfall |
+| [ACP snapshot replay](../../../acp/snapshot-replay.md) | curated | snapshot harness behavior |
 
-### Why one generator
+### Why generators own the docs
 
-Keeping the atlas behind one generator gives reviewers one freshness gate and keeps cross-page terminology synchronized. The tradeoff is that curated diagrams are edited in TypeScript string blocks rather than directly in Markdown. That is acceptable for this first cut because the user-facing artifact is still plain Markdown/Mermaid, and a future change can split the curated pages out if authorship ergonomics matter more than one-command regeneration.
+Package topology stays in `gen-module-graph.ts`, and tool-package affordances stay in `gen-tool-catalog.ts`, because those generators already own the canonical facts and freshness gates. `gen-doc-graphs.ts` owns the remaining relationship pages and the index. The tradeoff is that curated diagrams are edited in TypeScript string blocks rather than directly in Markdown. That is acceptable for this first cut because the user-facing artifact is still plain Markdown/Mermaid, and a future change can split the curated pages out if authorship ergonomics matter more than regeneration.
 
 ### Completeness guards
 
 The hybrid pages must fail loud when their manifests are stale:
 
+- The module graph reads every package's `peerDependencies` and groups each package by its `packages/<group>/<pkg>` path.
+- The tool catalog boot-harvests shipped tools and renders the package/service/effect map from the same manifest that its completeness guard already checks.
 - The capability seam graph imports the Cordis service collector and asserts every discovered harness `ctx.<key>` is classified in `SERVICE_ROLES`, and every classified key still exists.
-- The tool affordance graph boot-harvests the shipped tool catalog and asserts every tool package has `TOOL_PACKAGE_META`.
 - The event producer/consumer matrix labels itself hybrid because subagent lifecycle events deliberately use `ctx.events.dispatch` for per-listener containment; those dynamic edges are explicit overrides rather than invisible omissions.
 - `verify-mermaid` parses every repo-authored ` ```mermaid ` fence with Mermaid's own parser, so syntax errors fail `doc-sync` locally and in CI instead of showing up as broken GitHub-rendered diagrams.
 
@@ -61,7 +61,7 @@ Use Mermaid for committed diagrams because GitHub renders it in Markdown and it
 
 ## Consequences
 
-- Maintainers get visual entry points for topology, seams, event flow, lifecycle, session replay, and snapshot behavior.
+- Maintainers get visual entry points for topology, seams, event flow, lifecycle, app composition, and snapshot behavior.
 - SDK users get a path from use case to package composition instead of only bottom-up package references.
 - `doc-sync` now includes `verify-doc-graphs` and `verify-mermaid`, so graph drift and Mermaid syntax errors are caught with the other doc freshness gates.
-- Future fs and hooks work has a concrete place to land new complexity: fs should expand the capability and tool graphs, while hooks should expand the event matrix and tool execution pipeline.
+- Future fs and hooks work has a concrete place to land new complexity: fs should expand the capability docs and tool catalog, while hooks should expand the event matrix and tool execution pipeline.