Docs: use relative cross-doc links now that website#4385 has landed

Background

nf-core/website#4385 was merged on 2026-09-02 and fixes nf-core/website#4384.

Until then, relative links between a pipeline's own docs pages 404'd on the website.
Docs pages are served at trailing-slash URLs (/magmap/dev/docs/output/), and the site's markdown rewriter only stripped the .md extension, leaving the href relative.
So usage.md#anchor written in docs/output.md resolved one level too deep, to /magmap/dev/docs/output/usage, which does not exist.
GitHub rendered the same source correctly, which is why this went unnoticed for years.

Because of that, several nf-core pipelines — magmap included — write cross-references between their own docs pages as absolute https://nf-co.re/... URLs instead.
That is no longer necessary, and the relative form is now strictly better.

See nf-core/phyloplace#83 for the same cleanup on phyloplace, with the fuller write-up.

What works now

A relative link to another docs/*.md page is rewritten at build time into a root-relative, version-preserving URL:

docs/output.md:  [Choosing an annotator](usage.md#choosing-an-annotator-prokka-or-bakta)

  read on /magmap/dev/docs/output/    -> /magmap/dev/docs/usage/#choosing-an-annotator-prokka-or-bakta
  read on /magmap/1.0.0/docs/output/  -> /magmap/1.0.0/docs/usage/#choosing-an-annotator-prokka-or-bakta

The reader stays on whichever version channel they were browsing, and the link still renders correctly on GitHub.

This is preventive, not a bug fix

magmap has no broken links today.
Both cross-doc anchors currently resolve on the released pages:

released magmap output page, #summary-tables                        present=1
released magmap usage page,  #choosing-an-annotator-prokka-or-bakta present=1

The reason to change them anyway is that an absolute https://nf-co.re/magmap/<page> link always resolves to the released docs.
The moment one of these anchors points at a section that only exists on dev, the link starts returning 200 and silently dropping the reader at the top of the page with no anchor jump — a failure nobody reports, because it does not look like an error.
That has already happened on phyloplace; see #83 for the evidence.

Doing it now, while both links happen to work, is cheap and means the trap is not there later.

What to change

Two links, both cross-references between our own docs pages:

file	line	current target	should become
docs/usage.md	330	https://nf-co.re/magmap/output#summary-tables	output.md#summary-tables
docs/output.md	126	https://nf-co.re/magmap/usage#choosing-an-annotator-prokka-or-bakta	usage.md#choosing-an-annotator-prokka-or-bakta

Line numbers are against dev at the time of writing; grep for the URLs rather than trusting them.

What to leave absolute

• The ~12 https://nf-co.re/magmap/parameters/#... links in docs/usage.md and docs/output.md.
  The parameters page is generated from nextflow_schema.json and has no markdown source file, so there is no relative form to write.
  It has the same version-pinning weakness — an anchor for a parameter added on dev will not resolve until release — but nothing in this repo can fix that.
• The results page and anything else outside docs/.
• The template banner at the top of docs/usage.md (## :warning: Please read this documentation on the nf-core website: ...).
  It is deliberately absolute, since its job is to move a reader off GitHub, and it is template boilerplate.
• Links in README.md and docs/CONTRIBUTING.md, which are read mostly on GitHub.

How to verify

The website deploys on its own schedule and /dev/ docs lag a merge, so check after a deploy rather than immediately.

1. Open https://nf-co.re/magmap/dev/docs/output/ — note the trailing slash, which is the form the docs tabs link to and the one where the old bug appeared.
2. Click each changed link.
3. Each should land on the matching /magmap/dev/docs/<page>/#<anchor> and scroll to the section, staying on dev.

Checking from https://nf-co.re/magmap/output (short, no trailing slash) is not a valid test: relative links resolved correctly from that URL form even while the bug was live, which is exactly why it stayed hidden.

Search docs/usage.md and docs/output.md for the two https://nf-co.re/magmap links identified in the issue. Replace only the cross-document links with the specified relative targets, leaving parameters, results, template, README.md, and CONTRIBUTING.md links unchanged. After a website deploy, verify from the trailing-slash /magmap/dev/docs/ pages that both links preserve dev and reach their anchors.