Opt-in destructive command. Deletes the persistent local clone cache that DISCOVER and REFRESH populate under ~/.cache/skill-engine/. Always dry-runs first; only deletes after explicit user confirmation.

Usage

/skill-engine:clean-cache [kind]

kind is optional:

omitted → clean every cache subtree under ~/.cache/skill-engine/, including old flat-layout entries.
git-managed → clean only ~/.cache/skill-engine/git-managed/.
web-doc → clean only ~/.cache/skill-engine/web-doc/.

Always prompts with a list of directories before deletion. No deletion happens without confirmation.

What gets deleted

Everything under ${XDG_CACHE_HOME:-$HOME/.cache}/skill-engine/. The cache is partitioned by source kind:

~/.cache/skill-engine/git-managed/<source_id>-<sha>/ — shallow clones of git-backed upstream sources at a specific SHA.
~/.cache/skill-engine/web-doc/<source_id>-<crawl_id>/ — snapshots of crawled web documentation for a specific crawl.

Old flat-layout entries (~/.cache/skill-engine/<source_id>-<sha>/) may still exist if they predate the kind-partitioned layout and have not yet been migrated by REFRESH; this command will clean them too. The cache is regenerable: a subsequent DISCOVER or REFRESH against the same upstream re-creates whatever it needs from gh/git or the web crawler.

Nothing outside the cache root is touched. No contextualizer state (.claude/skills/<slug>-context/, including its research/ and references/ directories) is touched. No user files outside ~/.cache/skill-engine/ are touched.

Workflow

cache_root="${XDG_CACHE_HOME:-$HOME/.cache}/skill-engine"

if [ ! -d "$cache_root" ]; then
  printf '%s\n' "Cache root not present at $cache_root — nothing to clean."
  exit 0
fi

# Parse optional [kind] argument.
kind="${1:-}"
case "$kind" in
  ""|git-managed|web-doc) ;;
  *)
    printf 'ERROR: invalid kind %q (expected: git-managed, web-doc, or omitted)\n' "$kind" >&2
    exit 2
    ;;
esac

Step 1: Dry-run preview

List the entries that would be deleted, scoped by $kind if set. Default to dry-run only — emit the list without deleting.

total=$(du -sh "$cache_root" 2>/dev/null | awk '{print $1}')
printf '%s\n' "Cache root: $cache_root"
[ -n "$kind" ] && printf '%s\n' "Kind filter: $kind"
printf '%s\n' "Total size: ${total:-0}"
printf '\n%-60s  %8s  %s\n' "Directory" "Size" "Last accessed"

# Build the list of directories in scope.
if [ -z "$kind" ]; then
  # All kinds + any legacy flat-layout entries at the cache root.
  scan_globs=( "$cache_root"/git-managed/*/ "$cache_root"/web-doc/*/ "$cache_root"/*/ )
else
  scan_globs=( "$cache_root/$kind"/*/ )
fi

for d in "${scan_globs[@]}"; do
  [ -d "$d" ] || continue
  base="$(basename "$d")"
  # Skip the kind subdirectories themselves when caught by the bare */ glob.
  if [ -z "$kind" ]; then
    [ "$base" = "git-managed" ] && continue
    [ "$base" = "web-doc" ] && continue
  fi
  sz=$(du -sh "$d" 2>/dev/null | awk '{print $1}')
  accessed=$(stat -f '%Sa' -t '%Y-%m-%d' "$d" 2>/dev/null \
             || stat -c '%x' "$d" 2>/dev/null | cut -d' ' -f1)
  name="${d#"$cache_root"/}"
  name="${name%/}"
  printf '%-60s  %8s  %s\n' "$name" "$sz" "$accessed"
done

Surface the listing and ask the user to confirm. The confirmation phrasing should make the destructive scope explicit and name the kind filter when set:

Delete the listed directories (total: )? [if kind set:] Filter: only <kind> cache subtree. Reply yes to proceed, anything else to abort.

If the user does not reply with the literal word yes, abort without deleting.

Worked example. A typical dry-run with no kind filter, surfaced before the confirmation prompt, looks like:

Cache root: /Users/me/.cache/skill-engine
Total size: 135M

Directory                                                         Size  Last accessed
git-managed/django-django-cccc3333                                31M   2026-04-28
git-managed/vitejs-vite-aaaa1111                                  52M   2026-05-11
git-managed/vitejs-vite-bbbb2222                                  52M   2026-05-12
web-doc/anthropic-docs-eeee5555                                   42M   2026-05-15
legacy-flat-dddd4444                                              18M   2026-03-02

Delete the listed directories (total: 135M)?
A subsequent /skill-engine:discover or /skill-engine:refresh against any of
these sources will re-clone or re-crawl from upstream when run.

Reply `yes` to proceed, anything else to abort.

Two directories with the same <source_id> prefix (here, vitejs-vite-*) indicate REFRESH has not yet GC'd the older SHA — the older directory is stale and safe to remove. Entries directly under the cache root (here, legacy-flat-dddd4444) are pre-migration flat-layout cache; REFRESH's pre-flight step 1.5 normally relocates them on the next run.

When invoked with a [kind] argument, the preview lists only that subtree:

$ /skill-engine:clean-cache web-doc
Cache root: /Users/me/.cache/skill-engine
Kind filter: web-doc
Total size: 42M

Directory                                                         Size  Last accessed
web-doc/anthropic-docs-eeee5555                                   42M   2026-05-15

Step 2: Deletion (only after confirmation)

if [ -z "$kind" ]; then
  # All kinds + legacy flat-layout entries.
  rm -rf -- "$cache_root"/git-managed/*/ "$cache_root"/web-doc/*/
  # Legacy flat entries (anything else directly under cache_root that is
  # a directory but not 'git-managed' or 'web-doc').
  for d in "$cache_root"/*/; do
    [ -d "$d" ] || continue
    base="$(basename "$d")"
    [ "$base" = "git-managed" ] && continue
    [ "$base" = "web-doc" ] && continue
    rm -rf -- "$d"
  done
else
  rm -rf -- "$cache_root/$kind"/*/
fi

Notes:

The -- guards against any subdirectory name starting with -.
Do NOT delete the cache root itself, nor the git-managed/ or web-doc/ kind subdirectories themselves — only their children.
Do NOT follow symlinks. The */ glob expands only to directories, but be conservative: a symlinked directory should be inspected before deletion. If unsure, skip it.
Do NOT delete anything outside the cache root, ever. The literal string ${XDG_CACHE_HOME:-$HOME/.cache}/skill-engine/ must appear verbatim in the deletion path; never substitute, never accept user-supplied paths beyond the validated kind enum.

Step 3: Post-clean summary

After deletion, emit a one-line summary: "Deleted N directories, freed ." If a subsequent DISCOVER or REFRESH runs, it will re-clone or re-crawl from upstream into a fresh kind-partitioned directory (~/.cache/skill-engine/git-managed/<source_id>-<sha>/ or ~/.cache/skill-engine/web-doc/<source_id>-<crawl_id>/).

When to suggest this command

The user may want to clean the cache when:

A contextualizer is finished and no REFRESH cycles are planned.
Disk usage is a concern and /skill-engine:status shows accumulated cache directories.
The user has rotated to a different project and the cached sources are no longer relevant.

This command is opt-in: nothing in the engine invokes it automatically.

What this skill does NOT do

It does not delete contextualizer state (no .claude/skills/*-context/ directory is touched).
It does not delete source-paths.json or any references/ files.
It does not unregister sources.
It does not delete ~/.cache/skill-engine/ itself, only its immediate children.
It does not run DISCOVER or REFRESH afterward — the user runs those separately when ready.

Invariants

Dry-run is the default; deletion requires explicit yes.
Deletion scope is bounded to ${XDG_CACHE_HOME:-$HOME/.cache}/skill-engine/*/.
No network access. No state writes to any contextualizer. Read-then-delete only.