FE-1509: Add the notebook view's data model and layout foundations

[kube]

🌟 What is the purpose of this PR?

First data layer of the Notebook view stack, stacked on #9429: the pure projections the view renders from. No UI changes — nothing here is reachable until the next layer lands.

🔗 Related links

• FE-1509 (internal)

🔍 What does this change?

• notebook-model: projects an SDCPN into a flat cell list and a single dependency-edge index covering all five entity kinds; both gutter directions derive from the same edges so they cannot disagree. Parameter usage is a word-boundary text match against transition and equation code.
• notebook-order: topological cell ordering that inlines each type, equation and parameter just before its first user, without ever dropping a cell.
• net-graph-layout: a cut-down Sugiyama layered layout (DFS cycle-breaking, longest-path layering, barycentre ordering) plus a focus mode that re-layers by hop distance from one node, with unreachable components keeping their own layered band.
• The notebook layer's architecture-docs README.

The structural analyses (cycles, initial places) are deliberately not here — they arrive above the view in #9431/#9432 for separate review.

Pre-Merge Checklist 🚀

🚢 Has this modified a publishable library?

This PR:

• does not modify any publishable blocks or libraries, or modifications do not need publishing
  • one patch changeset for the whole stack ships in the top PR

📜 Does this require a change to the docs?

The changes in this PR:

• are in a state where docs changes are not yet required but will be
  • this is tracked in: the user-docs PR at the top of this stack

🕸️ Does this require a change to the Turbo Graph?

The changes in this PR:

• do not affect the execution graph

🛡 What tests cover this?

notebook-model.test.ts (cell projections, connection index, fuzzy match, dependent counts, net graph), notebook-order.test.ts (inlining, unused declarations, never dropping cells), net-graph-layout.test.ts (layering, cycle breaking, focus mode, edge geometry, determinism).

❓ How to test this?

1. npx turbo run test:unit --filter @hashintel/petrinaut

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Project	Deployment	Actions	Updated (UTC)
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[semgrep-code-hashintel]

Semgrep found 1 detect-non-literal-regexp finding:

• libs/@hashintel/petrinaut/src/ui/views/Notebook/notebook-model.ts
  • L202 - Triage

RegExp() called with a variableName function argument, this might allow an attacker to cause a Regular Expression Denial-of-Service (ReDoS) within your application as RegExP blocks the main thread. For this reason, it is recommended to use hardcoded regexes instead. If your regex is run on user-controlled input, consider performing input validation or use a regex checking/sanitization library such as https://www.npmjs.com/package/recheck to verify that the regex does not appear vulnerable to ReDoS.

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PR Summary

Low Risk
New, untested-in-prod modules under ui/views/Notebook with no app integration; behavior is covered by unit tests and does not alter existing editor or mutation paths.

Overview
Adds the pure data layer for the experimental Notebook view: no UI wiring yet, so nothing user-facing changes until follow-up PRs land.

notebook-model projects an active net into flat cells (all five entity kinds), a single dependency connection index (arcs, types, equations, word-boundary parameter references in code), token-flow buildNetGraph, neighbourhood splitting for cycles, dependent counts, and fuzzy name search for cell filtering.

notebook-order implements topological list ordering: places/transitions follow a supplied flow order (e.g. from the diagram), with types, equations, and parameters inlined once before their first user; unused or off-graph cells are appended, never dropped.

net-graph-layout lays out the whole-net graph from arcs only (ignores canvas x/y): DFS cycle breaking, longest-path layering, barycentre ordering, optional focus re-layering (upstream above, downstream below), SVG edgePath for forward drops and bowed return edges.

Includes architecture README and broad Vitest coverage for all three modules.

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