Post-migration cleanup: finish what the rename left behind

[splaisan]

A rename is not finished when the rename succeeds. GitHub's redirect keeps every leftover working, so nothing fails and no check turns red — which is exactly why the leftovers survive. This ticket lists what is left in Nucleomics-VIB/plotting-tools, measured on 2026-09-03, and it is worked in this repo's own session.

The rule this comes from, with the detection commands and the reasoning: Nucleomics-VIB/SP_AI_skills -> studies/github_repo_renaming/post_migration_rule.md. Umbrella ticket for the branch half: Nucleomics-VIB/SP_AI_skills#64.

What applies here

item	applies	measured
Default branch is master	yes	master
GitHub Pages builds from master	no	no Pages site
/master/ URLs to relink	yes	1 into this repo, 0 elsewhere
Repo was renamed	no	name unchanged
Old name in a URL	no	0 line(s)
Old name in docs	no	0 line(s)
Old name in build/deploy files	no	0 line(s)
Old name in code/scripts	no	0 line(s)
Old name in history files	no	0 line(s)
Branch protection	MISSING	no ruleset — see #63
Self-hosted runner	no	-
Stale local checkout	none found	0 outside /opt/github/

1 /master/ URL(s) — relink in the SAME pass as the branch rename

file	line	URL	breaks when
basic_demux_QC/basic_demux_QC.Rmd	10	https://github.com/Nucleomics-VIB/plotting-tools/tree/master/basic_demux_QC	this repo renames its branch

The pass, in order

• Re-run the detection block from post_migration_rule.md — the numbers above are one point in time.
• Rename the branch: gh api -X POST repos/Nucleomics-VIB/plotting-tools/branches/master/rename -f new_name=main
• Rewrite the 1 /master/ URL(s) to /main/ — same pass as the branch rename, not a follow-up.
• Fetch every URL you changed: curl -s -o /dev/null -w '%{http_code}' -L <url> must print 200.
• This repo has no ruleset — master/main can be force-pushed or deleted by anyone with write access. That is #63, not this ticket, but a migration session is the cheapest moment to close it.
• Close this ticket quoting the verified 200s.

Not urgent

Nothing here is broken today. Every old URL answers through the redirect and no check is red. That is precisely the risk: this decays quietly, and it is cheapest to fix while the rename is fresh.