[rudycelekli]

What was wrong

Four reference links in skills currently return HTTP 404 (checked 2026-10-14 with curl -L):

File	Dead link	Working replacement
skills/pacsomatic/references/pacsomatic_guide.md	docs.seqera.io/nextflow/executor/{lsf,pbspro,sge}	docs.seqera.io/nextflow/reference/executor/{lsf,pbspro,sge} (200; these are the targets linked from the live executor overview page)
skills/scanpy/references/upstream-review.md	.../en/stable/generated/scanpy.pp.neighbors.html	.../en/stable/api/generated/scanpy.pp.neighbors.html (200)
skills/pennylane/references/advanced_features.md	docs.pennylane.ai/en/stable/code/qml_templates.html	docs.pennylane.ai/en/stable/introduction/templates.html (200)
skills/scientific-slides/assets/powerpoint_design_guide.md	gitbrent.github.io/PptxGenJS/docs/ (2 places)	gitbrent.github.io/PptxGenJS/ (200)

I extracted every URL from the n-z skills' markdown and checked status codes; these were the only dead documentation pages that are not intentional (e.g. the documented pypi.org/pypi/tiledbvcf/json 404 in tiledbvcf is deliberate and left alone). Does not overlap with #260.

Testing

• Re-fetched each replacement URL: all return 200.
• pytest tests/pacsomatic: 60 passed (scanpy/pennylane suites need their native deps, not installed here; the change is docs-only links).

🤖 Generated with Claude Code

[rahul05ranjan]

Verified all the claimed 404s and replacements independently — everything checks out.

What I ran (static + curl -L status checks; I did not run the test suites):

• Confirmed all 7 dead links exist on main at the cited spots: pacsomatic_guide.md:63-65 (executor/lsf, executor/pbspro, executor/sge), upstream-review.md:75 (scanpy.pp.neighbors), advanced_features.md:182 (code/qml_templates.html), powerpoint_design_guide.md:16 and :639 (PptxGenJS /docs/). All four old URL patterns return 404, all four replacements return 200.
• Grepped the whole repo after applying the patch: no remaining occurrences of any of the dead patterns, so the fix is complete rather than partial.
• Checked the neighbors of the fixed links to make sure this isn't a wholesale URL migration: the other scanpy /stable/generated/ links in the same list (highly_variable_genes, pca, leiden) and the other code/... PennyLane links (qml_noise, ParametrizedEvolution) all still return 200 — so neighbors genuinely moved to /api/generated/ and qml_templates.html to introduction/templates.html. The PennyLane replacement also matches what quantum_ml.md:147 already links on main, which is good corroboration.
• docs.seqera.io/nextflow/executor (kept at line 60) is still live, consistent with your note that the three deep links are what the overview page now points to.

One tiny observation, no action needed: in upstream-review.md the neighbors entry now sits in the same bullet list as links using the plain /generated/ path — the inconsistency is real on scanpy's side, not yours.

Overlap with your other PRs (#307, #308, #311) in case maintainers are triaging the batch: #310 touches none of the same files, so it merges independently of all three. However, #307 and #311 both rewrite the same BIDS Starter Kit line in skills/bids/SKILL.md:215 with different targets (#307 → bids-website.readthedocs.io/.../getting_started/index.html, #311 → github.com/bids-standard/bids-starter-kit; old link 404, both replacements 200) — whoever merges second will need a rebase, and it'd be worth picking one canonical target up front.