feat: add repository knowledge atlas

[lsjfy-open-com]

Summary

This adds a repository-local knowledge layer and a bundled, read-only topology atlas on top of CodeGraph's existing graph:

• index Markdown headings as section nodes without changing or replacing any existing code extraction
• resolve local Markdown links and conservative inline-code symbol mentions into exact persisted references edges
• expose bounded, exact induced graph snapshots and exact node neighborhoods
• add codegraph ui [path] with bundled offline assets, loopback-only defaults, semantic/directory/language grouping, progressive labels, node/edge filters, visual-only group aggregation, and a precise inspector

Why

Repository knowledge is split between source and local documents. Agents and humans need to move from architecture/runbooks to concrete symbols while retaining the original CodeGraph identity and relationship truth. Existing node IDs, qualified names, edge endpoints, edge kinds, and code extraction paths remain unchanged; document nodes are appended and UI aggregation is presentation-only.

Related work

• feat(markdown): index documentation graph links #361 also indexes Markdown. This PR intentionally uses a smaller V1 surface (headings, local links, unambiguous symbol mentions) and combines it with the topology API/UI. I am happy to rebase the UI on feat(markdown): index documentation graph links #361, split the PR, or reuse its richer extractor if maintainers prefer.
• feat: add codegraph view — interactive zoomable HTML graph #1198 adds a self-contained codegraph view. This PR uses a loopback read-only service instead, so search and the inspector query the full SQLite graph while the browser renders a bounded snapshot. The atlas emphasizes macro distribution before node-level inspection.

User impact

cd your-project
codegraph init
codegraph ui --limit 1200
# open http://127.0.0.1:7474

No CDN, external document fetch, or runtime network dependency is introduced. External URLs stay as source text and are not crawled.

Validation

• npm run build
• 606/606 existing extraction tests
• 618/618 extraction + Markdown + wire-contract + topology tests
• 98/100 security, watcher, and CLI tests (2 existing platform skips)
• WSL Rust kernel: 15/15 tests
• real-browser validation on Graphify: 10,717 nodes / 25,441 edges; grouping, filtering, zoom labels, search, direct selection, and exact inspector relationships; 0 console errors/warnings and localhost-only requests

Design notes are included under docs/design/repository-documents-v1.md and docs/design/repository-topology-ui-v1.md.