diff --git a/scripts/sync-plugin-content.sh b/scripts/sync-plugin-content.sh
index 0adb9fd..0cd1ee2 100755
--- a/scripts/sync-plugin-content.sh
+++ b/scripts/sync-plugin-content.sh
@@ -46,6 +46,12 @@ set -euo pipefail
 # The merged hooks file is mirrored like the other MIRROR_DIRS content: synced when
 # .apm/hooks/ produces one, and removed (real mode) / flagged as drift (--check) when
 # it no longer does but a mirrored copy is still sitting there from a prior sync.
+# The hooks/ directory holding it is owned outright by the mirror the same way every
+# MIRROR_DIRS destination is -- a real sync wipes and rebuilds it, so a stray file
+# dropped inside, or the empty directory left behind once .apm/hooks/ stops producing
+# a hooks.json, is cleaned up rather than preserved. (A stray at the PLUGIN ROOT is a
+# different matter and stays out of scope by design: README.md, docs/, bin/, .mcp.json
+# and friends are hand-authored there.)
 # It lands at hooks/hooks.json, not at the plugin root: Claude Code convention-scans
 # `hooks/hooks.json` "at the plugin root, not inside .claude-plugin/"
 # (plugins/kyberforge/docs/research/docs/claude-code-plugins/configuration.md's "Plugin
@@ -106,17 +112,30 @@ if ! command -v jq &>/dev/null; then
 fi
 
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-# shellcheck source=lib/marketplace-plugins.sh
+# Both source= paths below are repo-root-relative, not script-dir-relative -- see
+# tests/run-tests.sh for why the script-dir spelling silently fails to resolve.
+# shellcheck source=scripts/lib/marketplace-plugins.sh
 source "$SCRIPT_DIR/lib/marketplace-plugins.sh"
-# shellcheck source=lib/batch-run.sh
+# shellcheck source=scripts/lib/batch-run.sh
 source "$SCRIPT_DIR/lib/batch-run.sh"
 
 # Convention subdirectories apm's plugin exporter can populate from .apm/.
+#
+# These are DESTINATION directory names at the plugin root, not .apm/ source
+# directory names -- the two lists are deliberately not the same, so do not "fix"
+# this by pasting in the header comment's .apm/ list. In particular .apm/prompts/
+# has no destination of its own: apm's exporter folds it into commands/ together
+# with .apm/commands/, renaming *.prompt.md to *.md (ADR-0017's mapping table;
+# re-verified empirically against apm 0.28.0, and pinned by the prompts test in
+# tests/test-sync-plugin-content.sh). Adding `prompts` here would name an output
+# directory apm never emits and no plugin host ever scans.
 MIRROR_DIRS=(agents skills commands instructions extensions)
 
-# Where the merged hooks file lands (Claude Code's convention-scanned path), and
-# the pre-fix root-level path a real sync now cleans up as stale.
-HOOKS_REL="hooks/hooks.json"
+# The generated hooks directory, the merged hooks file inside it (Claude Code's
+# convention-scanned path), and the pre-fix root-level path a real sync now cleans
+# up as stale.
+HOOKS_DIR_REL="hooks"
+HOOKS_REL="$HOOKS_DIR_REL/hooks.json"
 LEGACY_HOOKS_REL="hooks.json"
 
 FAIL=0
@@ -202,15 +221,24 @@ sync_hooks_json() {
     rm -f "$legacy"
   fi
 
+  # hooks/ is generated output the mirror owns outright, exactly like every
+  # MIRROR_DIRS destination -- so wipe it wholesale and rebuild, rather than
+  # editing hooks.json in place and leaving whatever else happens to be in there.
+  # sync_dir gets this for free from its own rm -rf; hooks/ has to spell it out
+  # because its one legitimate occupant is written by name instead of copied as a
+  # tree. The wipe covers both a stray file someone dropped alongside hooks.json
+  # and the case where .apm/hooks/ stops producing a hooks.json at all: the
+  # directory then ends up absent, not present-and-empty.
+  #
+  # ${target_dir:?} rather than a bare expansion: `set -u` aborts on an UNSET
+  # variable but not an empty one, and an empty $target_dir would make this
+  # `rm -rf /hooks`. The other rm -rf calls here take a $dst built by their
+  # caller; this one is the only place a bare parameter is the whole prefix.
+  rm -rf "${target_dir:?}/$HOOKS_DIR_REL"
+
   if [[ -f "$src" ]]; then
-    mkdir -p "$target_dir/hooks"
+    mkdir -p "$target_dir/$HOOKS_DIR_REL"
     normalize_trailing_newline "$src" "$dst"
-  elif [[ -f "$dst" ]]; then
-    # .apm/hooks/ no longer produces a hooks.json, but one is still sitting at
-    # $dst from a prior sync -- that's stale mirrored output, not "no .apm/hooks/
-    # content" (which would mean $dst never existed in the first place).
-    rm -f "$dst"
-    rmdir "$target_dir/hooks" 2>/dev/null || true
   fi
 }
 
@@ -290,6 +318,14 @@ path_manifest() {
 # symlink to identical content, both leave --check at exit 0 while a real sync
 # silently repairs them -- check and sync disagreeing, which is the one thing this
 # gate exists to prevent. Compare an explicit type+exec-bit manifest as well.
+#
+# The manifest is a full recursive listing, so it is also what makes an entry that
+# exists on only one side visible. That is the sole coverage the generated hooks/
+# directory gets for anything other than hooks.json itself (which check_file above
+# handles by name): a stray file inside hooks/, or hooks/ still sitting there empty
+# after .apm/hooks/ stopped producing anything, shows up here as a manifest line
+# present on one side only. Both are things sync_hooks_json's rm -rf removes, so
+# both have to be drift.
 check_path_modes() {
   local plugin_dir="$1" expected_dir="$2"
   shift 2
@@ -299,7 +335,7 @@ check_path_modes() {
   path_manifest "$expected_dir" "$@" >"$expected"
   path_manifest "$plugin_dir" "$@" >"$actual"
   if ! diff -q "$expected" "$actual" >/dev/null 2>&1; then
-    echo "DRIFT $plugin_dir: mirrored file types/modes differ from a fresh sync" >&2
+    echo "DRIFT $plugin_dir: mirrored paths/types/modes differ from a fresh sync" >&2
     diff "$expected" "$actual" 2>&1 | sed 's/^/    /' >&2 || true
     FAIL=1
   fi
@@ -426,7 +462,10 @@ sync_one() {
     # not apm's own Copilot-ecosystem output (which omits it).
     reinject_mcp_servers "$plugin_dir" "$pack_cwd"
     local -a checked_paths
-    checked_paths=("${MIRROR_DIRS[@]}" "$HOOKS_REL" "$LEGACY_HOOKS_REL")
+    # $HOOKS_DIR_REL, not $HOOKS_REL: the manifest comparison has to see the whole
+    # generated directory (see check_path_modes), and listing it recursively already
+    # covers hooks/hooks.json.
+    checked_paths=("${MIRROR_DIRS[@]}" "$HOOKS_DIR_REL" "$LEGACY_HOOKS_REL")
     for d in "${MIRROR_DIRS[@]}"; do
       check_dir "$plugin_dir" "$pack_cwd" "$d"
     done
diff --git a/tests/test-sync-plugin-content.sh b/tests/test-sync-plugin-content.sh
index 69fe1b0..a3bf90f 100755
--- a/tests/test-sync-plugin-content.sh
+++ b/tests/test-sync-plugin-content.sh
@@ -17,7 +17,9 @@ fi
 # Minimal fixture exercising every mirrored category -- all five of
 # scripts/sync-plugin-content.sh's MIRROR_DIRS (agents, skills, commands,
 # instructions, extensions) plus the merged hooks file -- without needing network
-# access (no apm.yml dependencies). Two deliberately-shaped skill subdirectories:
+# access (no apm.yml dependencies). It also carries a .apm/prompts/ entry, which has
+# no MIRROR_DIRS destination of its own: apm folds prompts into commands/. Two
+# deliberately-shaped skill subdirectories:
 #
 #   skills/hello/tests/                    -- a dev-time fixture that must NOT be mirrored
 #   skills/hello/assets/templates/tests/   -- a template asset that MUST be mirrored
@@ -34,7 +36,7 @@ make_fixture() {
   mkdir -p "$dir/.apm/skills/hello/tests" "$dir/.apm/skills/hello/scripts" \
     "$dir/.apm/skills/hello/assets/templates/tests" "$dir/.apm/agents" \
     "$dir/.apm/hooks" "$dir/.apm/commands" "$dir/.apm/instructions" \
-    "$dir/.apm/extensions"
+    "$dir/.apm/extensions" "$dir/.apm/prompts"
   cat > "$dir/apm.yml" <<'YAML'
 name: fixture
 version: 0.0.1
@@ -81,6 +83,12 @@ EOF
 description: mycmd
 ---
 Do a thing.
+EOF
+  cat > "$dir/.apm/prompts/greet.prompt.md" <<'EOF'
+---
+description: greet
+---
+Greet the user.
 EOF
   cat > "$dir/.apm/instructions/style.instructions.md" <<'EOF'
 ---
@@ -539,6 +547,98 @@ else
   fi
 fi
 
+# --- 20. .apm/prompts/ is mirrored, via commands/ rather than a prompts/ of its own ---
+# The script header lists prompts among the .apm/ directories it mirrors while
+# MIRROR_DIRS has no `prompts` entry, which reads as a hole and has already been filed
+# as one. It is not: MIRROR_DIRS names DESTINATION directories, and apm's exporter
+# folds .apm/prompts/ into commands/ (renaming *.prompt.md to *.md) alongside
+# .apm/commands/. This pins that mapping, so an apm upgrade that gave prompts a
+# destination of its own — the one change that would genuinely need a MIRROR_DIRS
+# entry — fails here instead of silently dropping the content.
+echo ""
+echo "--- .apm/prompts/ content arrives in commands/, not in a prompts/ directory ---"
+FIXTURE20="$(make_fixture)"; track "$FIXTURE20"
+bash "$SCRIPT" "$FIXTURE20" > /dev/null 2>&1
+if [[ -f "$FIXTURE20/commands/greet.md" ]]; then
+  pass ".apm/prompts/greet.prompt.md is mirrored to commands/greet.md"
+else
+  fail ".apm/prompts/ content never reached commands/ — apm's prompts mapping changed"
+fi
+if [[ ! -e "$FIXTURE20/prompts" ]]; then
+  pass "no prompts/ directory is produced at the plugin root"
+else
+  fail "a prompts/ directory appeared at the plugin root — it now needs a MIRROR_DIRS entry"
+fi
+if bash "$SCRIPT" --check "$FIXTURE20" > /dev/null 2>&1; then
+  pass "--check is clean with .apm/prompts/ content present"
+else
+  fail "--check reports drift on a freshly synced fixture carrying .apm/prompts/"
+fi
+
+# --- 21. A stray file inside the generated hooks/ directory is drift ---
+# hooks/ is mirror-owned output, so it is scoped like a MIRROR_DIRS destination and
+# not like the plugin root (where README.md, docs/, bin/ and .mcp.json are all
+# hand-authored and deliberately none of this script's business). Before hooks/ came
+# under that ownership, --check exited 0 on a stray inside it and a real sync left the
+# stray untouched — agreeing with each other, but agreeing on the wrong answer.
+echo ""
+echo "--- a stray file inside the generated hooks/ directory is reported and removed ---"
+FIXTURE21="$(make_fixture)"; track "$FIXTURE21"
+bash "$SCRIPT" "$FIXTURE21" > /dev/null 2>&1
+if [[ ! -f "$FIXTURE21/hooks/hooks.json" ]]; then
+  fail "initial sync did not create hooks/hooks.json -- can't test the stray case"
+else
+  printf '{"stray": true}\n' > "$FIXTURE21/hooks/extra.json"
+  if bash "$SCRIPT" --check "$FIXTURE21" > /dev/null 2>&1; then
+    fail "no drift reported for a stray file inside the generated hooks/ directory"
+  else
+    pass "a stray file inside hooks/ is reported as drift"
+    bash "$SCRIPT" "$FIXTURE21" > /dev/null 2>&1
+    if [[ ! -e "$FIXTURE21/hooks/extra.json" ]] && [[ -f "$FIXTURE21/hooks/hooks.json" ]]; then
+      pass "re-sync removes the stray and keeps hooks/hooks.json"
+    else
+      fail "re-sync did not clean the stray out of hooks/"
+    fi
+    if bash "$SCRIPT" --check "$FIXTURE21" > /dev/null 2>&1; then
+      pass "re-sync clears the stray-hooks-file drift"
+    else
+      fail "re-sync did not clear the stray-hooks-file drift"
+    fi
+  fi
+fi
+
+# --- 22. An empty leftover hooks/ directory is drift, not an acceptable resting state ---
+# When .apm/hooks/ produces no hooks.json, the correct mirror state is no hooks/
+# directory at all — not an empty one. Empty leftovers are exactly what earlier
+# revisions of this script left behind in this repo's own plugin roots.
+echo ""
+echo "--- an empty leftover hooks/ directory is reported and removed ---"
+FIXTURE22="$(make_fixture)"; track "$FIXTURE22"
+rm -rf "$FIXTURE22/.apm/hooks"
+bash "$SCRIPT" "$FIXTURE22" > /dev/null 2>&1
+if [[ -e "$FIXTURE22/hooks" ]]; then
+  fail "sync created hooks/ for a plugin whose .apm/hooks/ produces no hooks.json"
+else
+  pass "no hooks/ directory when .apm/hooks/ produces nothing"
+fi
+mkdir -p "$FIXTURE22/hooks"
+if bash "$SCRIPT" --check "$FIXTURE22" > /dev/null 2>&1; then
+  fail "no drift reported for an empty leftover hooks/ directory"
+else
+  pass "an empty leftover hooks/ directory is reported as drift"
+  bash "$SCRIPT" "$FIXTURE22" > /dev/null 2>&1
+  if [[ ! -e "$FIXTURE22/hooks" ]]; then
+    pass "re-sync removes the empty leftover hooks/ directory"
+  else
+    fail "re-sync left the empty hooks/ directory in place"
+  fi
+  if bash "$SCRIPT" --check "$FIXTURE22" > /dev/null 2>&1; then
+    pass "re-sync clears the empty-hooks-directory drift"
+  else
+    fail "re-sync did not clear the empty-hooks-directory drift"
+  fi
+fi
+
 echo ""
 echo "Results: $PASS passed, $FAIL failed"
 [[ $FAIL -eq 0 ]]