SKILL.md

$28

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:

Read the full content

Extract existing wikilinks — find all [[...]] references already present

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

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

Signal

Points

Example

Exact name match in text

"MyProject" appears in body text → link to my-project.md

Shared tags (2+)

Both tagged #ai #agent but no link between them

Same project, no link

Both under projects/my-project/ but don't reference each other

Mentioned entity/concept

Page mentions "knowledge graphs" → link to [[concepts/knowledge-graphs]]

Cross-category connection

Source is in concepts/, target is in entities/ (or skills/ ↔ synthesis/) — different knowledge layers make this link more architecturally valuable

Peripheral→hub reach

Source page has ≤ 2 total links (peripheral) but target has ≥ 8 (hub) — connecting a loose page to a load-bearing concept

Partial name match

"graph" appears but page is knowledge-graphs — plausible but ambiguous

Confidence labels

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

Score

Label

Action

≥ 6

EXTRACTED

Link is effectively certain — exact mention or very strong match. Apply inline.

3–5

INFERRED

Link is a reasonable inference — shared context, cross-category, peripheral→hub. Apply inline or as Related section.

1–2

AMBIGUOUS

Weak or partial match. Skip unless user specifically asks to connect loose pages.

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):

Sentence pattern

Inferred type

"X extends / builds on / generalises Y"

extends

"X implements / is an implementation of Y"

implements

"X contradicts / opposes / refutes / is at odds with Y"

contradicts

"X is derived from / based on / adapted from Y"

derived_from

"X uses / relies on / depends on / requires Y"

uses

"X replaces / supersedes / deprecates Y"

replaces

Shared tags or cross-category inference with no directional cue

related_to

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 pages in misc/ (pages with promotion_status: misc in their frontmatter, or located under the misc/ directory).

For each misc page:

Collect outgoing links — all [[wikilinks]] in the page body

Collect incoming links — grep the vault for [[misc/<slug>]] and [[<slug>]] references

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

Group by project name and sum: outgoing_links + incoming_links

Update the affinity frontmatter block on the misc page:

affinity:

  obsidian-wiki: 3

  another-project: 1

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

Pages in misc/ that have ≥ 3 connections to a single project — ready to be promoted:

| Page | Top Project | Score |

|---|---|---|

| `misc/web-martinfowler-articles-microservices.md` | `obsidian-wiki` | 4 |

To promote: move the page to `projects/<project-name>/references/` and update all backlinks.

### 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

QMD is a search index, not the source of truth. If $QMD_WIKI_COLLECTION is empty or unset, skip this step. Run it only after this skill has written or rewritten vault markdown. If QMD refresh fails, do not roll back the vault changes; report the QMD status separately.

Use $QMD_CLI if set; otherwise use qmd.

${QMD_CLI:-qmd} update

If the output says vectors are needed or embeddings may be stale, run:

${QMD_CLI:-qmd} embed

Verify the collection with either:

${QMD_CLI:-qmd} ls "$QMD_WIKI_COLLECTION"

or, when a specific page path is known:

${QMD_CLI:-qmd} get "qmd://$QMD_WIKI_COLLECTION/<page>.md" -l 5

Record one of:

QMD refreshed: update + embed + verified

QMD refreshed: update only + verified

QMD skipped: QMD_WIKI_COLLECTION unset

QMD skipped: qmd CLI unavailable

QMD failed: <short error summary>

cross-linker