Wikilink Integrity

When to Use This Skill

Use this skill when...	Use the alternative instead when...
Repairing broken `[[Target]]` wikilinks after a note rename or move	Discovering which links Obsidian flags as unresolved in the first place — use `search-discovery`
Resolving cross-namespace ambiguity between `Zettelkasten/` and `work/z/` notes	Reorganising or merging the work-namespace stub itself — use `vault-stubs`
Unqualifying path-prefixed `[[Kanban/X]]` links to bare basenames	Reconnecting orphan notes that have no links at all — use `vault-orphans`

Obsidian resolves [[Target]] by looking for a note whose basename is Target.md anywhere in the vault. Links break silently when a note is renamed, moved, or was never created. Ambiguity arises when two notes share a basename.

Link Syntax

[[Note Name]]                      # basename resolution
[[Note Name|Alias]]                # custom display text
[[Note Name#Section heading]]      # deep link to heading
[[folder/Note Name]]               # path-qualified (usually unnecessary)
![[Image.png]]                     # embed (image, note, PDF)

Resolution Rules

Unqualified target ([[Docker]]) resolves to any note with basename Docker.md. If two exist (e.g. Zettelkasten/Docker.md and work/z/Docker.md), Obsidian picks one non-deterministically — ambiguous.
Path-qualified target ([[Kanban/Main]]) resolves to Kanban/Main.md exactly — no basename fallback.
Embeds (![[X]]) follow the same resolution. Image embeds typically target files under Files/.

Common Breakage Patterns

Pattern	Fix
`[[OldTopic]]` × many → note doesn't exist	Rewrite to `[[Topic]]` (the actual note)
`[[Development MOC]]` → note was renamed	Rewrite to `[[Development Workflows and Tools MOC]]`
`[[Kanban/X]]` → works but path-qualified is brittle	Rewrite to `[[X]]` when basename is unique
`[[code]]`, `[[project]]` → never were real notes	These were inline-tag syntax errors; delete the link and leave plain text
`[[Gen AI Some Idea]]` (double space)	Fix the extra whitespace in the link

Cross-Namespace Ambiguity

When two notes share a basename (e.g. Docker.md in both Zettelkasten/ and work/z/), every [[Docker]] in the vault becomes ambiguous. Options:

Rename one so they stop colliding (work/z/Docker.md → keep as redirect stub; content lives in Zettelkasten/Docker.md).
Path-qualify the links that should resolve to the non-canonical copy: [[work/z/Docker]].
Never use bare [[Docker]] going forward; always path-qualify.

The preferred pattern is #1: keep canonical content in Zettelkasten/, make work/z/ a tiny redirect stub.

Detection

# Build a set of note basenames
fd -e md -x basename {} .md

# Find all wikilinks
rg -o '\[\[([^\]|#]+)' --no-filename --glob '*.md'

# Broken links: pipe the above through comm(1) against the basename set

A more accurate scan uses the links.analyze_links analyzer in vault-agent, which handles aliases, sections, and embeds correctly.

Offline Fallback (App Closed)

The detection methodology above is unchanged — only the data source changes when Obsidian (and its obsidian CLI / live link index) is closed. The obsidian CLI and vault-agent analyzers are the live-index path; parsing the .md corpus directly with the rg/fd Detection snippet above is the deterministic headless default, and for batch/scheduled audits it is often the better choice (reproducible, free of app/index state). vault-frontmatter already operates this way.

Parse the corpus directly:

Frontmatter — read each note's YAML block between the leading --- fences; extract tags, aliases, context. See vault-frontmatter for YAML-block mechanics.
Wikilinks — match [[Target]], [[Target|Alias]], [[Target#Heading]], [[folder/Target]], and ![[embed]]. Resolve each target to a note by basename, then relative path, then alias (from frontmatter), all case-insensitive. Resolve ![[embed]] against attachments as well as notes — the attachment folder is per-vault configurable, so read it from .obsidian/app.json (attachmentFolderPath) and fall back to the vault root / Files/ only when that key is unset.

A link is broken when its target resolves to no note after the basename → relpath → alias (case-insensitive) cascade — embeds against attachments included. A target is ambiguous when its basename matches 2+ notes (the cross-namespace case above). Feed the Detection snippet's output through this resolution cascade to reproduce the unresolved audit headlessly.

Rewriting Strategy

For a known-broken target with many references, rewrite in one commit:

fix(links): rewrite 44 × [[OldTopic]] → [[Topic]]

Use Edit with replace_all=True for the target string within each note. Don't use shell sed — it doesn't handle the frontmatter / codeblock boundary correctly, and Edit's per-file atomicity makes the commit review straightforward.

For small-count broken targets (1–2 references each), report them and let the user decide whether to delete the link, create the note, or redirect.

Ambiguous-Target Handling

Never auto-rewrite an ambiguous link. Report the ambiguity with both candidates and ask the user which resolution they want:

[[Docker]] in Zettelkasten/Kubernetes.md → candidates:
  a) Zettelkasten/Docker.md
  b) work/z/Docker.md (redirect stub)

Safety

Never rewrite links inside code blocks or YAML frontmatter.
Never auto-create missing target notes — that's a content decision, not a maintenance one.
Preserve the alias form: [[Ansible|my ansible]] → [[Ansible|my ansible]], not [[Ansible]].

Related Skills

vault-orphans — notes with no links at all
vault-mocs — structured outgoing-link hubs
search-discovery — runtime link traversal via Obsidian CLI

vault-wikilinks