For skills.sh.json, your file location looks right because it is at the repo root:
niebag/skills/skills.sh.json
and the skill slugs you used also look like they match the current skills shown on the repo page.
The part that may be confusing is that skills.sh.json only controls how the repo page is displayed/grouped. It does not remove skills from the index, and it does not change what the CLI installs.
The docs also mention that skills.sh picks up skills.sh.json after the repository is seen by telemetry, usually after someone installs from the repo with the skills CLI, and that repo pages are cached:
So I’d try one fresh install after the config was added, then wait for the cache/index to refresh:
npx skills add niebag/skills
If the page still does not update after that, I’d open an issue with these exact details:
Repo: niebag/skills
Config file: https://github.com/niebag/skills/blob/main/skills.sh.json
Expected: grouped repo page using Engineering / Project Management
Actual: default flat list still shown
Also stale/removed skills are still listed
Last install/test time:
For removed skills specifically, I would not expect deleting files from GitHub to immediately remove old telemetry/index entries. That probably needs a reindex or cleanup on the skills.sh side if the stale entries remain visible.