Link Health — Repo-wide Markdown Link Audit Methodology

A reusable methodology for bringing a broken docs-heavy repo's link checker to green. Codified from a real audit that took AlterLab-IEU/AlterLab-Academic-Skills from 1208 errors out of 1966 links to 0 errors out of 1912 links across 8 commits, with an auto-detected Tier 3 regression that validated the guardrail rule.

Quick Start

Full audit (fresh repo, failing link checker):

Audit and repair the link health of <owner/repo>. Run the full four-tier pipeline.

→ Dispatch the 10-agent audit from playbooks/full-audit.md, then the tiered APPLY phase.

Targeted residual pass (first dispatch reduced errors but some remain):

The link checker is down from 1208 to 67 errors. Close the residuals.

→ Dispatch the 3-agent followup pass from playbooks/followup-pass.md.

Post-merge cleanup (PR is green, need to finalize human-decision items):

Finalize the post-merge cleanup: resolve pending human-decision items, file follow-up issues, document link debt.

→ Dispatch the 4-agent post-merge pass from playbooks/post-merge.md.

---

Trigger Conditions

Trigger Keywords

English: link audit, dead links, link health, lychee, broken links, link checker, markdown link audit, link-health audit, 404 audit, check-links failing, CI link-check

繁體中文: 連結健檢, 死鏈, 失效連結, 斷鏈檢查, 連結審計

When This Skill Applies

• A weekly Check Links (or similar lychee / markdown-link-check) workflow has been failing.
• The user mentions a large error count (hundreds+) that they suspect is mostly config-driven false positives.
• The user wants to refactor broken intra-repo file references across many skills / docs.
• The user wants a reusable process for link debt maintenance going forward.

Non-Trigger Scenarios

Scenario	Skill / Tool to Use Instead
Fix a single broken link in a single file	Direct Edit — no pipeline needed
Add a new URL to skill docs	alterlab-scientific-writing or the relevant domain skill
Verify a bibliography actually exists (DOI/author resolution, fabricated/hallucinated citations)	alterlab-citation-verifier — it cross-checks Crossref/OpenAlex/Semantic Scholar/arXiv. Link-health only repairs broken hyperlinks in docs; it never validates that a cited work exists.
Audit repo structure beyond links (schema, metadata)	Separate schema-drift audit (out of scope)

---

Pipeline Overview (4 Tiers)

Each tier is a single reviewable commit. Run them in order — each unlocks the next by making the error signal cleaner.

Tier	Scope	Typical Delta
1 — Config	Introduce .lychee.toml with an additive accept set, a .lycheeignore for permanent noise hosts, and a hardened CI workflow.	Biggest single win — often -70% to -90% of errors. Fixes the "--accept 403 replaces the default set" gotcha.
2 — Intra-repo refs	Repair [ERROR] file:// entries: singular/plural directory typos, missing path prefixes, YAML frontmatter bugs. Wrap pedagogical placeholder paths as inline code.	Eliminates the bulk of real breakage — usually 200-400 entries collapse to zero.
3 — URL substitutions	Replace MOVED external URLs with verified-live substitutes; replace DEAD_INFRA URLs with replacement resources. Never substitute without verification.	Reduces residuals to the low dozens.
4 — Exclusions	Everything left that cannot be fixed: bot-hostile hosts, pedagogical placeholders, expired upstream infrastructure, chronically flaky academic sites.	Gets to 0 errors or stable single-digit residuals.

See references/tier1-config.md through references/tier4-exclusions.md for the decision rules in each tier.

---

The Tier 3 Guardrail

After any URL substitution pass, re-run the link checker and diff against the baseline success set. Any URL that returned 200 OK in baseline and is non-200 after substitution is a regression and MUST be reverted before commit.

Self-check:

diff <(grep "^\[200\]" baseline.log | sort -u) \
     <(grep "^\[200\]" post.log | sort -u)

Output should show no deletions, only additions. Deletions mean a substitution regressed a previously-working URL.

This rule exists because during the source audit, broad sed prefix substitutions silently concatenated onto more-specific paths (e.g. /v3/ → /v3/docs turned an already-correct /v3/docs into /v3/docsdocs). The guardrail caught it on the second CI dispatch, not the commit itself. Assume your Tier 3 pass will have regressions. Verify.

Full detail: references/tier3-substitution.md.

---

The Verification-First Rule

DEFAULT to probe-verification before any URL substitution. Unverified substitutions are how phantom URLs land in public skills. Before every [old] → [new] replacement:

1. For GitHub repos: gh api repos/owner/name — status must be 200 (repo exists, not archived).
2. For HTTP URLs: curl -sSI -L --max-time 15 '<new>' — final status must be 200 (after redirects).
3. For PyPI / npm / crates packages: check the registry API or landing page directly.

If verification fails, exclude the dead target via .lycheeignore with a commented reason rather than guessing a replacement. An excluded dead link is honest; a substituted wrong link is a time bomb.

Full detail: references/tier3-substitution.md § "Verification rules".

---

Playbooks

Three ready-to-dispatch prompt bundles that call this skill's tiers in the right order.

Playbook	When to Use	Agents
playbooks/full-audit.md	Fresh audit, failing CI, no prior work.	10 parallel subagents + synthesis
playbooks/followup-pass.md	Errors significantly reduced but residuals remain.	3 targeted subagents
playbooks/post-merge.md	PR green, time to resolve pending human-decision items.	4 parallel subagents

All three follow the same shape: pre-flight → parallel dispatch → synthesize → commit/PR/merge → verify.

---

References

File	Content
references/tier1-config.md	.lychee.toml schema, workflow YAML, accept-code gotchas
references/tier2-intra-repo.md	Intra-repo path audit, singular/plural directory patterns, frontmatter fixes
references/tier3-substitution.md	URL substitution rules, the guardrail, sed-safety patterns
references/tier4-exclusions.md	When to exclude vs substitute, .lycheeignore category rubric
references/known-debt-template.md	The 5-category KNOWN_LINK_DEBT.md layout for maintainers

---

Examples

• examples/pr-1-retrospective.md — the source audit that generated this skill. 1208 → 0 errors, 8 commits, auto-detected Tier 3 regression in commit 5 (9cbd801), merged as 93a72fe.

---

Scope Discipline

This skill fixes link health. It does NOT:

• Standardize SKILL.md schemas across the repo. File schema drift as a separate issue.
• Refactor skill content, examples, or prose. Only touches link URLs and the CI config.
• Modify .lychee.toml's accept list to mask real breakage. Flaky upstream 5xx / timeouts get excluded per-host with rationale, not blanket-accepted.

Scope discipline keeps the PR reviewable and the link-check signal honest.