A repository-cleanup tool that finds entries in repos.yaml whose repository folders are missing, then removes them from the configuration and its matching documentation after confirmation.

Use it to scan repos/repos.yaml, review missing repository folders, and remove confirmed stale entries from repos.yaml and repos.md.

It prevents the workspace list from referring to folders that no longer exist. It also avoids manually keeping the configuration and repository notes in sync.

How raffertyuy/repo-of-repos configures Claude Code

Reuse

Borrowing it

Nothing to install: this file belongs to raffertyuy/repo-of-repos. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file

curl -O https://raw.githubusercontent.com/raffertyuy/repo-of-repos/main/.agents/skills/clean-repos/SKILL.md

Clone the repo

git clone --depth 1 https://github.com/raffertyuy/repo-of-repos

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/raffertyuy/repo-of-repos/clean-repos/github.svg)](https://agentmods.dev/skills/raffertyuy/repo-of-repos/clean-repos)

Your own site

<a href="https://agentmods.dev/skills/raffertyuy/repo-of-repos/clean-repos"><img src="https://agentmods.dev/badge/skills/raffertyuy/repo-of-repos/clean-repos/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/raffertyuy/repo-of-repos/clean-repos"><img src="https://agentmods.dev/badge/skills/raffertyuy/repo-of-repos/clean-repos.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 19 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 596 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00019	$0.00596
Opus 5	$0.00010	$0.00298
Sonnet 5	$0.00004	$0.00119
Haiku 4.5	$0.00002	$0.00060

Measured 12d ago against content hash 70f6066777fc, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

clean-repos scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 12d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.agents/skills/clean-repos/SKILL.md · 53 lines

How it starts

The opening of the file, as written. The whole thing — 53 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Clean Repos

Scan repos/repos.yaml for stale entries — entries whose corresponding repos/<name>/ directory no longer exists on disk — and remove them from the configuration.

Order of Operations

Parse repos/repos.yaml — read the repos: list
- If the list is empty, report "Nothing to clean" and stop
Check each entry — for every entry, check if repos/<name>/ exists on disk
Collect stale entries — entries where the directory does NOT exist
- If no stale entries found, report "All entries are present on disk. Nothing to clean." and stop
Show the stale entries — display a table:

Entry Type URL Status

<name> git <url> Directory missing

<name> local — Directory missing
Ask for confirmation — "Remove these N entries from the config? (yes/no)"
- If the user says no, stop without changes
Remove stale entries from repos/repos.yaml — delete each stale entry from the repos: list
- If all entries were stale, leave repos: []
Remove stale entries from repos/repos.md — for each stale entry, delete its ## <name> section and all content up to the next ## heading or end of file
- If no entries remain, restore the placeholder: 
Update .gitignore — for each stale entry, if repos/<name>/ appears in .gitignore (whether git repo or gitignored local folder), remove the line. No need to ask — stale entries shouldn't leave gitignore debris.
Report a summary:

Entry Type Action

<name> git Removed from repos.yaml, repos.md, .gitignore

<name> local Removed from repos.yaml, repos.md (and .gitignore if present)

Entry	Type	URL	Status
`<name>`	git	`<url>`	Directory missing
`<name>`	local	—	Directory missing

Entry	Type	Action
`<name>`	git	Removed from repos.yaml, repos.md, .gitignore
`<name>`	local	Removed from repos.yaml, repos.md (and .gitignore if present)

Notes

This skill never deletes directories — it only cleans up config for directories that are already gone
The inverse scenario (directories exist but aren't in config) is handled by /pull-all-repos orphan detection
Always confirm before making changes — never auto-remove
Safe to run as a dry-run check: if there are no stale entries, it just reports "nothing to clean"

Read the full file on GitHub · 53 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

12d ago First seen · 53 lines · 19 tokens per session scan A 70f6066777fc

Subscribe to this mod's changes

clean-repos is a skill published in the GitHub repository raffertyuy/repo-of-repos (12 stars, last pushed 1mo ago), licensed MIT. It adds 19 tokens to every session and 596 once invoked, about $0.0001 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

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repo-of-repos: Skill for Claude Code