Cross-Linker — Automated Wiki Cross-Referencing

You are weaving the wiki's knowledge graph tighter by finding and inserting missing [[wikilinks]] between pages that should reference each other but currently don't.

Follow the Retrieval Primitives table in llm-wiki/SKILL.md. Build the registry in Step 1 by grepping frontmatter only (not full pages). Reserve full Read for the unlinked-mention detection pass, and even there, only read pages whose summaries/titles make them plausible link targets. Blind full-vault reads are what this framework exists to avoid.

Before You Start

1. Resolve config — follow the Config Resolution Protocol in llm-wiki/SKILL.md (inline @name override → walk up CWD for .env → ~/.llm-wiki/config → prompt setup). This gives OBSIDIAN_VAULT_PATH and OBSIDIAN_LINK_FORMAT (default: wikilink).
2. Read index.md to get the full inventory of pages and their one-line descriptions
3. Skim log.md to see what was recently ingested (focus linking effort on new pages)

When inserting links in Step 4, apply the link format from llm-wiki/SKILL.md (Link Format section) using the OBSIDIAN_LINK_FORMAT value. When OBSIDIAN_LINK_FORMAT=markdown, compute the relative .md path from the file being edited to the target page.

Step 1: Build the Page Registry

Glob all .md files in the vault (excluding _archives/, .obsidian/). For each page, extract:

• Filename (without .md) — this is the wikilink target
• Title from frontmatter
• Aliases from frontmatter (if any)
• Tags from frontmatter
• Category from frontmatter or directory inference
• One-line summary — first sentence or title field

Build a lookup table:

page_name → { path, title, aliases, tags, summary }

This is your "vocabulary" — every entry in this table is a valid wikilink target.

Step 2: Scan for Missing Links

For each page in the vault:

1. Read the full content
2. Extract existing wikilinks — find all [[...]] references already present
3. Search for unlinked mentions — check if the page's text contains any of these, without being wrapped in [[...]]:
   • Page filenames (e.g., the word "MyProject" appears but [[projects/my-project/my-project]] is missing)
   • Page titles from frontmatter
   • Aliases from frontmatter
   • Entity names, project names, concept names from the registry
4. Check for semantic connections — pages that share multiple tags or are in the same project directory but don't link to each other

Matching Rules

• Case-insensitive matching for names (e.g., "my-project" matches page MyProject)
• Diacritic-insensitive matching — normalize both the page name and the body text with Unicode NFKD (decompose accented characters to base + combining marks, strip combining marks) before comparing. This ensures body text "Muller" matches page [[entities/müller]] and vice versa.
• Skip self-references — a page shouldn't link to itself
• Skip common words — don't link "the", "and", generic terms. Only match on distinctive names
• Prefer the shortest unambiguous wikilink path — use [[page-name]] not [[full/path/to/page-name]] when the name is unique across the vault
• Don't link inside code blocks or frontmatter
• Don't double-link — if [[foo]] already appears on the page, don't add another

Step 3: Score and Rank Suggestions

Not every possible link is worth adding. Score each candidate using a composite signal, then tag it with a confidence label.

Scoring

Confidence labels

Tag each candidate with a confidence label based on its score:

Only act on EXTRACTED and INFERRED candidates. Include the confidence label in the Cross-Link Report so the user can review INFERRED links before trusting them.

Step 4: Apply Links

For each page with missing links:

4a: Inline linking (preferred)

Find the first natural mention of the term in the body text and wrap it in wikilinks:

Before:

This project uses knowledge graphs to connect entities.

After:

This project uses [[concepts/knowledge-graphs|knowledge graphs]] to connect entities.

Use the [[path|display text]] format when the wikilink path differs from the display text.

4b: Related section (fallback)

If the term isn't mentioned naturally in the body but the pages are semantically related (shared tags, same project), add a ## Related section at the bottom of the page:

## Related

- [[projects/my-project/my-project]] — Also uses AI agents for research automation
- [[concepts/knowledge-graphs]] — Core technique used in this project

If a ## Related section already exists, append to it. Don't duplicate existing entries.

4c: Infer and write relationship type

For every EXTRACTED or INFERRED link added (inline or related section), infer a semantic relationship type from the surrounding sentence context and write it to the page's relationships: frontmatter block. Skip AMBIGUOUS links.

Type inference rules — scan the sentence containing the mention (or, for related-section links, the page title and shared-tag context):

If the surrounding context is ambiguous or the link came from shared-tag matching (no in-body mention), default to related_to.

Writing the block:

Read the page's YAML frontmatter. If a relationships: block already exists, append new entries without duplicating existing targets. If the block is absent, add it after aliases: (or after tags: when aliases: is missing).

relationships:
  - target: "[[concepts/knowledge-graphs]]"
    type: uses

Always use wikilink format ([[path/to/page]]) for target values in the relationships: YAML block — regardless of OBSIDIAN_LINK_FORMAT. The OBSIDIAN_LINK_FORMAT setting controls body content; frontmatter properties always use wikilink syntax so that wiki-export can reliably parse them.

Only add entries for links added in this cross-linker run — do not touch typed entries that were already present.

Step 5: Score Misc Page Affinity

After the main linking pass, update affinity scores for all misc pages: pages with promotion_status: misc in their frontmatter (URL ingests with no project home, kept in the reference folder), or — in older vaults — pages under a misc/ directory.

For each misc page:

1. Collect outgoing links — all [[wikilinks]] in the page body
2. Collect incoming links — grep the vault for [[misc/<slug>]] and [[<slug>]] references
3. For each linked page (both directions), check if it belongs to a project:
   • Lives under projects/<project-name>/
   • Has a project: frontmatter field matching a project name
4. Group by project name and sum: outgoing_links + incoming_links
5. Update the affinity frontmatter block on the misc page:

affinity:
  llm-wiki: 3
  another-project: 1

6. If any project's score ≥ 3: flag this page as a promotion candidate and record it for the report

Efficiency note: only read the full body of misc pages — other pages only need a frontmatter grep to determine their project membership.

Step 6: Report

Present a summary:

## Cross-Link Report

### Links Added: 23 across 12 pages

| Page | Links Added | Confidence | Placement | Relationship Types |
|---|---|---|---|---|
| `projects/my-project/my-project.md` | 3 | EXTRACTED | 2 inline, 1 related | uses ×2, related_to ×1 |
| `entities/jane-doe.md` | 5 | INFERRED | 3 inline, 2 related | extends ×1, uses ×3, related_to ×1 |
| ... | | | | |

### Orphan Pages Remaining: 2
- `references/foo.md` — no incoming or outgoing links found
- `concepts/bar.md` — could not find related pages

### Misc Promotion Candidates: N
Misc pages that have ≥ 3 connections to a single project — ready to be promoted:

| Page | Top Project | Score |
|---|---|---|
| `references/web-martinfowler-articles-microservices.md` | `llm-wiki` | 4 |

To promote: in a vault with a project folder, move the page to `projects/<project-name>/references/` and update all backlinks; without one, set `project: <project-name>` on the page and remove `promotion_status`.

### Pages Skipped: 3
- `index.md`, `log.md` — special files
- `_archives/*` — archived content

Step 7: Update Log and Hot Cache

Append to log.md:

- [TIMESTAMP] CROSS_LINK pages_scanned=N links_added=M typed_relations_written=T pages_modified=P orphans_remaining=Q misc_affinity_updated=R promotion_candidates=S

hot.md — Read $OBSIDIAN_VAULT_PATH/hot.md (create from the template in wiki-ingest if missing). Update Recent Activity with a one-line summary of what was linked — e.g. "Cross-linked 23 mentions across 12 pages; 2 orphans remain." Keep the last 3 operations. Update updated timestamp.

Tips

• Run after every ingest. New pages are almost always poorly connected. This is the fix.
• Be conservative with inline links. Only link the first natural mention, not every occurrence.
• Don't touch pages in _archives/. Those are frozen snapshots.
• Respect existing structure. If a page carefully curates its links in a ## Key Concepts section, add to that section rather than creating a separate ## Related.
• Entity pages are link magnets. An entity like jane-doe should be linked from almost every project page. Prioritize these.

QMD Refresh After Vault Writes

GUARD: If $QMD_WIKI_COLLECTION is unset — the default — skip this step. QMD is a search index, not the source of truth.

When it is set, read llm-wiki/references/qmd.md and follow the Refresh section after this skill has written vault markdown. If refresh fails, do not roll back the vault changes; report the QMD status separately.