fix: resolve wiki-root-relative wikilinks

[Mybigwang]

Summary

• Resolve wiki-root-relative wikilinks such as [[concepts/foo]] to existing wiki/concepts/foo.md pages.
• Keep support for existing bare links and project-relative wiki/... links.
• Apply the same resolution behavior across reader links, page links, structural lint, graph building, graph relevance, and the local API graph.

Why

LLM-generated wiki pages can emit links like [[concepts/foo]]. These links point to valid pages under wiki/concepts/, but some resolvers treated path-shaped links as project-relative only, causing false broken-link / missing-link reports and missing graph edges.

Tests

• npm run test:mocks -- src/lib/wiki-page-resolver.test.ts src/lib/lint-structural-core.test.ts src/lib/__tests__/wiki-graph.test.ts
• cargo test --manifest-path src-tauri/Cargo.toml commands::search::tests::page_links_require_markdown_input_and_exact_reader_paths
• cargo test --manifest-path src-tauri/Cargo.toml api_server::tests::resolve_link_accepts_wiki_root_relative_paths

[Copilot]

Pull request overview

This PR updates wikilink/path resolution so wiki-root-relative links like [[concepts/foo]] (and optional .md) correctly resolve to pages under wiki/ across the frontend resolver, structural lint, graph building/relevance, and the Tauri (Rust) link resolvers. This reduces false broken-link reports and restores missing graph edges for LLM-generated path-shaped links.

Changes:

• Extend resolveRelatedSlug to accept wiki-root-relative path refs (with/without .md) while still restricting resolution to wiki/.
• Update graph-building and relevance logic to normalize link targets and add path-based aliases (via per-node shortPath / basename) so concepts/foo resolves to the right node ID.
• Update structural lint indexing and Rust resolvers to recognize wiki-root-relative path-shaped links, plus add regression tests.

Reviewed changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/lib/wiki-page-resolver.ts	Adds support for wiki-root-relative path-shaped refs in resolveRelatedSlug.
src/lib/wiki-page-resolver.test.ts	Adds regression test for wiki-root-relative path refs with/without .md.
src/lib/wiki-graph.ts	Improves target indexing by adding shortPath and normalized aliases for path-shaped targets.
src/lib/lint-structural-core.ts	Expands normalization/indexing to resolve wiki-root-relative path-shaped links during structural lint.
src/lib/lint-structural-core.test.ts	Adds regression test ensuring structural lint doesn’t flag wiki-root-relative links as broken.
src/lib/graph-relevance.ts	Updates retrieval-graph link resolution to consider shortPath / basename normalization.
src/lib/tests/wiki-graph.test.ts	Adds regression test ensuring wiki-root-relative links produce graph edges.
src-tauri/src/commands/search.rs	Updates reader-links resolver to accept wiki-root-relative paths and optional .md.
src-tauri/src/api_server.rs	Updates API-server link resolver to accept wiki-root-relative/project-relative paths and optional .md.

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[Thomas-Piva]

Measured the impact of this on a vault built entirely by llm_wiki, in case it helps size the fix.

Test vault: 50 pages, generated end-to-end by the app from source ingest, no hand-authored links, no imported index convention. Its wiki/index.md contains 45 wikilinks, all in the [[entities/foo]] form the app itself writes in updateBoundedRecentIndexSection (path.replace(/^wiki\//, "")). Querying the local API graph for that project:

edges out of `index`:      0   (out of 45 links)
nodes with 0 links:        5
connected components:      6
orphans:                   14 / 50  (28%)

The index node is itself isolated in its own graph.

Control, same file and same role, on a second vault whose links had been converted to bare basenames:

vault	link form in index.md	edges from index
app-generated	[[entities/foo]]	0 / 45
basename-converted	[[foo]]	130

So this is not only cosmetic reporting noise. wiki/index.md is the one mechanism the app has for giving a freshly written page an inbound link, and because the writer and the resolvers disagree on the target form, none of those links become edges — which is where the 28% orphan rate on an otherwise healthy vault comes from (the generator itself averages 4.2 outgoing links per page, so the pages are not under-linked; nothing links back to them).

Worth noting the writer side too: updateBoundedRecentIndexSection caps that section at .slice(0, 200), so on a large vault the oldest entries fall out of the list regardless of how the links resolve.

Happy to re-run either measurement against this branch if that's useful.

[Mybigwang]

@Thomas-Piva
Thanks — this is really helpful context.
It makes the impact much clearer: this wasn’t just a reporting mismatch, it was preventing app-generated [[entities/foo]] links from turning into real graph edges.

The .slice(0, 200) cap is a separate writer-side limit, but the resolver fix should address the disconnected graph behavior you measured and eliminate most of the missing-link noise across nodes.