disk-hygiene

Disk Hygiene

Audit disk usage, clean developer caches, find forgotten large files, and triage Downloads on macOS.

Self-Evolving Skill: This skill improves through use. If instructions are wrong, parameters drifted, or a workaround was needed — fix this file immediately, don't defer. Only update for real, reproducible issues.

When to Use This Skill

Use this skill when:

• User asks about disk space, storage, or cleanup
• System is running low on free space
• User wants to find old/forgotten large files
• User wants to clean developer caches (brew, uv, pip, npm, cargo)
• User wants to triage their Downloads folder
• User asks about disk analysis tools (dust, dua, gdu, ncdu)

TodoWrite Task Templates

Template A - Full Disk Audit

1. Run disk overview (df -h /System/Volumes/Data && major directories)
2. Audit developer caches (uv, brew, pip, npm, cargo, rustup, Docker)
3. Scan in-repo build artifacts (Rust target/, .venv, node_modules — often the biggest, see Phase 2.5)
4. Scan for forgotten large files (>50MB, not accessed in 180+ days)
5. Present findings with AskUserQuestion for cleanup choices
6. Execute selected cleanups
7. Report space reclaimed

Template B - Cache Cleanup Only

1. Measure current cache sizes
2. Run safe cache cleanups (brew, uv, pip, npm)
3. Report space reclaimed

Template C - Downloads Triage

1. List Downloads contents with dates and sizes
2. Categorize into groups (media, dev artifacts, personal docs, misc)
3. Present AskUserQuestion multi-select for deletion/move
4. Execute selected actions

Template D - Forgotten File Hunt

1. Scan home directory for large files not accessed in 180+ days
2. Group by location and type (media, ISOs, dev artifacts, documents)
3. Present findings sorted by size
4. Offer cleanup options via AskUserQuestion

Phase 1 - Disk Overview

Get the lay of the land before diving into specifics.

/usr/bin/env bash << 'OVERVIEW_EOF'
echo "=== Disk Overview ==="
# MUST be /System/Volumes/Data, NOT `/`. On APFS (Catalina+) `/` is the SEALED
# READ-ONLY system volume and reports a fixed ~10GB used — it is not your disk.
# Verified 2026-07-31: `df -h /` said "10Gi used, 185Gi avail" on a machine that
# was actually 707GB used and 80% full. Reading `/` will make you conclude there
# is nothing to clean.
df -h /System/Volumes/Data

echo ""
echo "=== Major Directories ==="
du -sh ~/Library/Caches ~/Library/Logs ~/Library/Application\ Support \
  ~/.Trash ~/Downloads ~/Documents ~/Desktop ~/Movies ~/Music ~/Pictures \
  2>/dev/null | sort -rh

echo ""
echo "=== Developer Tool Caches ==="
du -sh ~/.docker ~/.npm ~/.cargo ~/.rustup ~/.local ~/.cache \
  ~/.conda ~/.pyenv ~/.local/share/mise 2>/dev/null | sort -rh
OVERVIEW_EOF

Phase 2 - Cache Audit & Cleanup

Cache Size Reference

Safe Cleanup Commands (Always Re-downloadable)

/usr/bin/env bash << 'CACHE_CLEAN_EOF'
set -euo pipefail

echo "=== Measuring current cache sizes ==="
echo "uv:       $(du -sh ~/Library/Caches/uv/ 2>/dev/null | cut -f1 || echo 'N/A')"
echo "Homebrew: $(du -sh ~/Library/Caches/Homebrew/ 2>/dev/null | cut -f1 || echo 'N/A')"
echo "pip:      $(du -sh ~/Library/Caches/pip/ 2>/dev/null | cut -f1 || echo 'N/A')"
echo "npm:      $(du -sh ~/.npm/_cacache/ 2>/dev/null | cut -f1 || echo 'N/A')"

echo ""
echo "=== Cleaning ==="
brew cleanup --prune=all 2>&1 | tail -3
uv cache prune 2>&1   # prune, NOT `clean --force` — see "uv cache lock" below
pip cache purge 2>&1
npm cache clean --force 2>&1
CACHE_CLEAN_EOF

Troubleshooting Cache Cleanup

⚠️ uv cache lock — never reach for --force before naming the holder

uv cache clean waits 300 s for an exclusive lock, then errors. Earlier revisions of this skill said "use --force". That advice is wrong when the lock holder is a long-running service, and it is the same class of mistake as the catgpt-gateway incident: mutating a cache underneath a live daemon.

Measured 2026-08-24: uv cache clean timed out, and the holders were

uv 1934  uv run python ~/eon/tasc/kernel/embed.py serve  --model minishlab/potion-retrieval-32M
uv 2652  uv run python ~/eon/tasc/kernel/embed.py rerank --serve --model Xenova/ms-marco-MiniLM-L-6-v2

— both children of the launchd job com.tasc.serve, up 1 h 37 m. These are persistent daemons, so the lock is never released and clean can never succeed on its own. Always identify the holder before deciding:

lsof ~/.cache/uv/.lock 2>/dev/null          # exact PIDs holding the lock
ps -o pid,ppid,lstart,command -p <PIDS>     # how long, and whose child
launchctl list | grep -i <service>          # is the parent a launchd job?

Then pick by holder:

Prefer uv cache prune over uv cache clean in routine hygiene. prune removes only unused entries and leaves everything a live environment depends on, so it is the correct periodic-maintenance verb; clean nukes everything and forces a full re-download.

uv archive-v0 silently accumulates whole virtual environments

The uv cache's headline number is misleading, so classify before you judge it. archive-v0 is documented as unpacked wheel bodies that get hardlinked into each .venv — that part earns its keep. But it also accretes complete virtual environments (build envs / tool envs) that are never garbage-collected, and those are pure dead weight. Measured 2026-08-24 on a 69 GB uv cache:

So 78 % of archive-v0 was orphaned environments, not the dedup layer. Classify it — the split changes both the diagnosis and the remedy (prune, not clean):

du -sk ~/.cache/uv/archive-v0/* 2>/dev/null > /tmp/uv-all.txt
while read -r kb path; do
  [ -f "$path/pyvenv.cfg" ] && echo "VENV $((kb/1024))MB $path"
done < /tmp/uv-all.txt | sort -k2 -rn | head

Also check hardlink counts before promising a number. uv hardlinks cache files into live .venvs, so deleting a cache entry with links>1 reclaims nothing:

stat -f 'links=%l size=%z %N' "$(find ~/.cache/uv/archive-v0 -type f -size +20M | head -1)"
# links=1 -> deleting truly reclaims;  links>1 -> shared with a live venv, no gain

Don't let "Python is bloated" be the conclusion. In the same audit, Rust's per-repo target/ dirs totalled 57 GB against ~7 GB of Python .venvs — 8× more — because target/ is per-repo with no sharing while uv's archive is shared across every project. Report the measured split, not the folk wisdom.

Phase 2.5 - Project Build Artifacts (in-repo, regenerable)

The single most-missed category — check it on EVERY audit. Compiler and dependency output lives inside your repos, not under ~/Library, so the Phase 1/2 scans never see it. A single active Rust repo's target/ routinely hits 10-35 GB; across a dev tree these artifacts can dwarf every cache combined (one real audit: 62 GB of target/ + 20 GB of .venv). All of it regenerates on the next build — the only cost is recompile / re-sync time.

Discover + size (point ROOTS at your code dirs)

/usr/bin/env bash << 'ARTIFACT_SCAN_EOF'
ROOTS=(~/eon ~/own ~/src ~/code ~/projects)
for n in target .venv node_modules .zig-cache zig-cache; do
  echo "=== $n (top 10 by size) ==="
  find "${ROOTS[@]}" -maxdepth 5 -type d -name "$n" -prune 2>/dev/null \
    -exec du -sh {} \; 2>/dev/null | sort -rh | head -10
done
ARTIFACT_SCAN_EOF

Safe deletion

Rust target/ — guard against false matches. Only delete a target/ that has a sibling Cargo.toml, so you never nuke an unrelated folder literally named "target":

/usr/bin/env bash << 'TARGET_CLEAN_EOF'
ROOTS=(~/eon ~/own)
find "${ROOTS[@]}" -maxdepth 5 -type d -name target -prune 2>/dev/null | while read -r t; do
  [ -f "$(dirname "$t")/Cargo.toml" ] && rm -rf "$t" && echo "cleaned: $t"
done
TARGET_CLEAN_EOF

.venv / node_modules are safe to bulk-delete by name (regenerated on next uv sync / install):

find ~/eon ~/own -maxdepth 5 -type d -name .venv -prune -exec rm -rf {} +

⚠️ CHECK FOR DEPENDENT SERVICES FIRST — this is not optional

node_modules and .venv are only "safe to bulk-delete" for repos nobody is running. On 2026-07-31 a bulk delete took out catgpt-gateway/node_modules; its launchd watchdog then failed 95 times and, in trying to restart the gateway, drove a Chrome launch that raised a macOS TCC prompt. The user reported it as a mysterious permission pop-up, and the disk cleanup was two steps removed from the symptom.

Build the exclusion list BEFORE deleting anything:

/usr/bin/env bash << 'DEPCHECK_EOF'
# Every repo backing a live launchd job — never delete artifacts inside these.
for p in "$HOME"/Library/LaunchAgents/*.plist; do
    prog=$(plutil -extract ProgramArguments.0 raw "$p" 2>/dev/null) || continue
    case "$prog" in "$HOME"/*) ;; *) continue ;; esac
    d=$(dirname "$prog")
    for _ in 1 2 3 4 5; do
        { [ -f "$d/package.json" ] || [ -f "$d/pyproject.toml" ]; } && break
        d=$(dirname "$d"); [ "$d" = "$HOME" ] && break
    done
    [ "$d" = "$HOME" ] && continue      # walked out; not a real repo match
    echo "$d"
done | sort -u
DEPCHECK_EOF

Then SKIP any candidate path under one of those roots, and print the skip so the operator can see the guard fired. After cleanup, re-run the same list and assert each repo still has the manifest-matching directory (package.json → node_modules, pyproject.toml → .venv).

⚠️ Check EVERY manifest in the repo, not just the one at the root. The version above walks up from the launchd program to the first package.json or pyproject.toml and stops — so for a repo whose service code lives in a subdirectory it verifies the wrong thing. Measured 2026-08-03 on ~/eon/tasc: the root has pyproject.toml (so the check reported .venv=ok and node_modules=—, i.e. "not applicable") while the service actually needs ts/node_modules, which was missing. The guard reported the repo healthy while its launchd job had been crash-looping 11,593 times. Enumerate instead:

find "$repo" -name package.json -not -path '*/node_modules/*' -maxdepth 3 \
  | while read -r m; do d=$(dirname "$m"); [ -d "$d/node_modules" ] || echo "MISSING $d/node_modules"; done
find "$repo" -name pyproject.toml -not -path '*/.venv/*' -maxdepth 3 \
  | while read -r m; do d=$(dirname "$m"); [ -d "$d/.venv" ] || echo "MISSING $d/.venv"; done

Also note a Python venv can be present and still incomplete: uv sync installs only the default dependency group. tasc declared its embedding deps under [dependency-groups] embed, so the venv existed, imported pymupdf fine, and failed on import numpy until uv sync --group embed was run. A directory existing is not the same as the dependencies being installed — where a repo documents a group/extra, restore it.

Caveats:

• Run pgrep -fl 'cargo build|rustc|zig build' first — never delete artifacts for a repo whose build/test is currently running.
• It's a regenerable-cost tradeoff: the next build is a cold rebuild (minutes for big Rust crates). Worth it for idle repos; skip the one repo you're about to build.
• cargo clean (run per-repo) is the tool-native equivalent of rm -rf target if you prefer.

Phase 3 - Forgotten File Detection

Find large files that have not been accessed in 180+ days.

/usr/bin/env bash << 'STALE_EOF'
echo "=== Large forgotten files (>50MB, untouched 180+ days) ==="
echo ""

# Scan home directory (excluding Library, node_modules, .git, hidden dirs)
find "$HOME" -maxdepth 4 \
  -not -path '*/\.*' \
  -not -path '*/Library/*' \
  -not -path '*/node_modules/*' \
  -not -path '*/.git/*' \
  -type f -atime +180 -size +50M 2>/dev/null | \
while read -r f; do
  mod_date=$(stat -f '%Sm' -t '%Y-%m-%d' "$f" 2>/dev/null)
  size=$(du -sh "$f" 2>/dev/null | cut -f1)
  echo "${mod_date} ${size} ${f}"
done | sort

echo ""
echo "=== Documents & Desktop (>10MB, untouched 180+ days) ==="
find "$HOME/Documents" "$HOME/Desktop" \
  -type f -atime +180 -size +10M 2>/dev/null | \
while read -r f; do
  mod_date=$(stat -f '%Sm' -t '%Y-%m-%d' "$f" 2>/dev/null)
  size=$(du -sh "$f" 2>/dev/null | cut -f1)
  echo "${mod_date} ${size} ${f}"
done | sort
STALE_EOF

Two traps when hunting big files

1. Apparent size ≠ allocated size (sparse files). ls -l and find -size report the file's logical extent; du reports blocks actually on disk. A corrupted index or a database with a runaway seek produces a sparse file where these differ by orders of magnitude. Measured 2026-08-03 on a ChromaDB HNSW file:

ls -l  link_lists.bin  ->  2831.5 GB   (apparent — impossible on a 926 GB disk)
du -h  link_lists.bin  ->  174 GB      (actual)

Always size candidates with du. If ls -l reports more than the disk holds, you have found a sparse file — and usually a bug worth reporting upstream, not just disk to reclaim. Never cp such a file (a naive copy expands the holes).

2. Applications quarantine their own wreckage — look for self-labelled dirs. Well-behaved data stores rename a damaged collection rather than deleting it, and the new name states the diagnosis. Grep the biggest directory for these markers:

find "$BIG_DIR" -maxdepth 2 -name '*corrupt*' -o -name '*.drift-*' \
     -o -name '*.pre-rebuild-*' -o -name '*.bak-*' -o -name '*.quarantine*'

Before deleting one, prove it is unreferenced and superseded:

• no live process holds an fd inside it — lsof -p <pid> | grep <dir> returns 0;
• the app's own index/manifest does not mention its UUID;
• a healthy replacement exists and the app has completed a run since.

Real case: ~/.mempalace had grown to 190 GB, of which 175 GB was one directory named <uuid>.corrupt-20260802-160712.drift-20260802-160712 — the app had already diagnosed and set aside the damage from a 3-day crash loop, and a healthy 882 MB collection had replaced it. Deleting it took the volume from 82 % to 60 % full in one command.

Common Forgotten File Types

Phase 4 - Downloads Triage

Use AskUserQuestion with multi-select to let the user choose what to clean.

Workflow

1. List all files in ~/Downloads with dates and sizes
2. Categorize into logical groups
3. Present AskUserQuestion with categories as multi-select options
4. Offer personal/sensitive PDFs separately (keep, move to Documents, or delete)
5. Execute selected actions

Categorization Pattern

/usr/bin/env bash << 'DL_LIST_EOF'
echo "=== Downloads by date and size ==="
find "$HOME/Downloads" -maxdepth 1 \( -type f -o -type d \) ! -path "$HOME/Downloads" | \
while read -r f; do
  mod_date=$(stat -f '%Sm' -t '%Y-%m-%d' "$f" 2>/dev/null)
  size=$(du -sh "$f" 2>/dev/null | cut -f1)
  echo "${mod_date} ${size} $(basename "$f")"
done | sort
DL_LIST_EOF

AskUserQuestion Template

When presenting Downloads cleanup options, use this pattern:

• Question 1 (multiSelect: true) - "Which items in ~/Downloads do you want to delete?"
  • Group by type: movie files (with total size), old PDFs/docs, dev artifacts, app exports
• Question 2 (multiSelect: false) - "What about personal/sensitive PDFs?"
  • Options: Keep all, Move to Documents, Delete (already have copies)
• Question 3 (multiSelect: false) - "Ongoing cleanup tool preference?"
  • Options: dust + dua-cli, Hazel automation, custom launchd script

Disk Analysis Tools Reference

Comparison (Benchmarked on ~632GB home directory, Apple Silicon)

Recommended Combo

• dust for quick "where is my space going?" - fastest scanner, tree output
• dua i or gdu-go for interactive exploration with deletion

Quick Usage

# dust - instant tree overview
dust -d 2 ~              # depth 2
dust -r ~/Library         # reverse sort (smallest first)

# dua - interactive TUI with safe deletion
dua i ~                   # navigate, mark, delete with confirmation

# gdu-go - ncdu-like TUI, fast on SSDs
gdu-go ~                  # full TUI with delete support
gdu-go -n ~              # non-interactive (for scripting/benchmarks)

Install All Tools

brew install dust dua-cli gdu

Note: gdu installs as gdu-go to avoid conflict with coreutils.

Quick Wins Summary

Ordered by typical space reclaimed (highest first):

Post-Change Checklist

After modifying this skill:

1. Cache commands tested on macOS (Apple Silicon)
2. Benchmark data still current (re-run if tools updated)
3. AskUserQuestion patterns match current tool API
4. All bash blocks use /usr/bin/env bash << 'EOF' wrapper
5. No hardcoded user paths (use $HOME)
6. Append changes to evolution-log.md

Troubleshooting

Hook-safe multi-line scripts

If the user's shell environment has bash hooks that intercept tool calls (pueue, asciinema, etc.) and the heredoc pattern fails with cryptic parse errors, write the script to a temp file and invoke it:

# Instead of: bash << 'EOF'  ... EOF
# Use: Write tool → /tmp/<task>.sh, then:
bash /tmp/<task>.sh

Single-line bash invocations like du -sh "$HOME/Library/Application Support"/Google/* 2>/dev/null | sort -rh | head work fine even with hooks installed — only multi-line heredocs containing spaced-path globs are problematic.

Post-Execution Reflection

After this skill completes, reflect before closing the task:

0. Locate yourself. — Find this SKILL.md's canonical path before editing.
1. What failed? — Fix the instruction that caused it.
2. What worked better than expected? — Promote to recommended practice.
3. What drifted? — Fix any script, reference, or dependency that no longer matches reality.
4. Log it. — Evolution-log entry with trigger, fix, and evidence.

Do NOT defer. The next invocation inherits whatever you leave behind.