diff --git a/scripts/check-manifests.sh b/scripts/check-manifests.sh
index 40ee6ce..930d23e 100755
--- a/scripts/check-manifests.sh
+++ b/scripts/check-manifests.sh
@@ -7,9 +7,18 @@ set -euo pipefail
 # Per ADR-0015, apm.yml is the authoring source and .claude-plugin/plugin.json is
 # compiled output with no skills/hooks/mcpServers/agents pointer fields (apm's plugin.json
 # builder deliberately omits them -- Claude Code auto-discovers those convention
-# directories, so listing them would be redundant/invalid). This script no longer checks
-# those fields; that's now scripts/sync-plugin-content.sh --check's job (drift between
-# .apm/ and the flat plugin-root mirror), wired as its own pre-push hook.
+# directories, so listing them would be redundant/invalid). For a plugin with an .apm/
+# directory, this script no longer checks those pointer fields itself; that's
+# scripts/sync-plugin-content.sh --check's job (drift between .apm/ and the flat
+# plugin-root mirror), wired as its own pre-push hook.
+#
+# sync-plugin-content.sh --check explicitly skips any plugin directory lacking .apm/
+# (an apm-native package it has nothing to compile), so that delegation leaves a real
+# gap for a non-apm plugin whose hand-authored plugin.json still uses the old
+# skills/hooks/mcpServers/agents pointer-field convention: nothing would check whether
+# those paths resolve. The fallback block below restores that check, but only for
+# plugins without .apm/ -- apm-native plugins keep relying on the delegation above so
+# the two checks don't duplicate (and disagree) on the same manifest.
 
 REPO_ROOT="${1:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"
 FAIL=0
@@ -26,32 +35,50 @@ if [[ ! -f "$MARKETPLACE" ]]; then
   exit 0
 fi
 
-plugin_count=$(jq '.plugins | length' "$MARKETPLACE")
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+# shellcheck source=lib/marketplace-plugins.sh
+source "$SCRIPT_DIR/lib/marketplace-plugins.sh"
 
-for ((i = 0; i < plugin_count; i++)); do
-  name=$(jq -r ".plugins[$i].name" "$MARKETPLACE")
-  source_type=$(jq -r ".plugins[$i].source | type" "$MARKETPLACE")
-
-  # Remote sources (github, git, npm objects) have no local directory to check
-  if [[ "$source_type" != "string" ]]; then
-    continue
-  fi
-
-  source=$(jq -r ".plugins[$i].source" "$MARKETPLACE")
-  source="${source#./}"
-  plugin_dir="$REPO_ROOT/$source"
+while IFS=$'\t' read -r name plugin_dir; do
+  source_rel="${plugin_dir#"$REPO_ROOT"/}"
 
   if [[ ! -d "$plugin_dir" ]]; then
-    err "plugin '$name': source directory not found: $source"
+    err "plugin '$name': source directory not found: $source_rel"
     continue
   fi
 
   manifest="$plugin_dir/.claude-plugin/plugin.json"
   if [[ ! -f "$manifest" ]]; then
-    err "plugin '$name': .claude-plugin/plugin.json not found in $source"
+    err "plugin '$name': .claude-plugin/plugin.json not found in $source_rel"
     continue
   fi
-done
+
+  # apm-native plugin: pointer-field validation is sync-plugin-content.sh --check's
+  # job (see header comment above).
+  [[ -d "$plugin_dir/.apm" ]] && continue
+
+  # Fallback for a non-apm plugin: validate that any skills/hooks/mcpServers/agents
+  # pointer fields in its hand-authored plugin.json still resolve to real paths.
+  skill_count=$(jq '.skills | if . then length else 0 end' "$manifest")
+  for ((s = 0; s < skill_count; s++)); do
+    skill_path=$(jq -r ".skills[$s]" "$manifest")
+    full_path="$plugin_dir/$skill_path"
+    full_path="${full_path%/}"
+    if [[ ! -d "$full_path" ]]; then
+      err "plugin '$name': skills path not found: $skill_path"
+    fi
+  done
+
+  for field in hooks mcpServers agents; do
+    ref=$(jq -r ".${field} // empty" "$manifest")
+    [[ -z "$ref" ]] && continue
+    full_path="$plugin_dir/$ref"
+    full_path="${full_path%/}"
+    if [[ ! -e "$full_path" ]]; then
+      err "plugin '$name': $field path not found: $ref"
+    fi
+  done
+done < <(list_marketplace_local_plugins "$REPO_ROOT" "$MARKETPLACE")
 
 if [[ $FAIL -gt 0 ]]; then
   echo "Manifest check failed: $FAIL error(s)" >&2
diff --git a/tests/test-check-manifests.sh b/tests/test-check-manifests.sh
index 633fc95..8180ff8 100644
--- a/tests/test-check-manifests.sh
+++ b/tests/test-check-manifests.sh
@@ -113,6 +113,97 @@ else
   pass "exits non-zero for a broken local entry even alongside a skipped remote entry"
 fi
 
+# --- 5. Non-.apm/ plugin with a broken pointer field is caught by the fallback path ---
+# apm-native plugins (.apm/ present) get their skills/hooks/mcpServers/agents
+# pointer-field validation from sync-plugin-content.sh --check instead (see this
+# script's header comment) -- but that script skips any plugin dir lacking .apm/
+# outright, so a non-apm plugin's hand-authored plugin.json needs this script's own
+# fallback validation to catch a broken pointer field.
+echo ""
+echo "--- catches a broken pointer field in a non-apm plugin's plugin.json ---"
+FIXTURE5="$(mktemp -d)"
+trap 'rm -rf "$FIXTURE5"' EXIT
+mkdir -p "$FIXTURE5/.claude-plugin"
+mkdir -p "$FIXTURE5/plugins/legacy/.claude-plugin"
+cat > "$FIXTURE5/.claude-plugin/marketplace.json" <<'JSON'
+{
+  "name": "test-marketplace",
+  "plugins": [
+    { "name": "legacy", "source": "./plugins/legacy" }
+  ]
+}
+JSON
+cat > "$FIXTURE5/plugins/legacy/.claude-plugin/plugin.json" <<'JSON'
+{
+  "name": "legacy",
+  "skills": ["./skills/does-not-exist"]
+}
+JSON
+if bash "$SCRIPT" "$FIXTURE5" > /dev/null 2>&1; then
+  fail "exited 0 for a non-apm plugin with a broken skills pointer -- expected exit 1"
+else
+  pass "catches a broken skills pointer field in a non-apm (no .apm/) plugin.json"
+fi
+
+# --- 6. Non-.apm/ plugin with valid pointer fields still passes (no false positive) ---
+echo ""
+echo "--- a non-apm plugin with valid pointer fields still passes ---"
+FIXTURE6="$(mktemp -d)"
+trap 'rm -rf "$FIXTURE6"' EXIT
+mkdir -p "$FIXTURE6/.claude-plugin"
+mkdir -p "$FIXTURE6/plugins/legacy-ok/.claude-plugin"
+mkdir -p "$FIXTURE6/plugins/legacy-ok/skills/real-skill"
+cat > "$FIXTURE6/.claude-plugin/marketplace.json" <<'JSON'
+{
+  "name": "test-marketplace",
+  "plugins": [
+    { "name": "legacy-ok", "source": "./plugins/legacy-ok" }
+  ]
+}
+JSON
+cat > "$FIXTURE6/plugins/legacy-ok/.claude-plugin/plugin.json" <<'JSON'
+{
+  "name": "legacy-ok",
+  "skills": ["./skills/real-skill"]
+}
+JSON
+if bash "$SCRIPT" "$FIXTURE6" > /dev/null 2>&1; then
+  pass "a non-apm plugin with a resolving skills pointer passes"
+else
+  fail "exited non-zero for a non-apm plugin whose pointer fields all resolve"
+fi
+
+# --- 7. An .apm/ plugin with a broken pointer field is NOT caught here (delegated) ---
+# Guards against the fallback path in finding #6 accidentally widening to also
+# validate apm-native plugins, which would duplicate (and could disagree with)
+# sync-plugin-content.sh --check's own drift detection.
+echo ""
+echo "--- an apm-native plugin's pointer fields are left to sync-plugin-content.sh --check ---"
+FIXTURE7="$(mktemp -d)"
+trap 'rm -rf "$FIXTURE7"' EXIT
+mkdir -p "$FIXTURE7/.claude-plugin"
+mkdir -p "$FIXTURE7/plugins/apm-plugin/.claude-plugin"
+mkdir -p "$FIXTURE7/plugins/apm-plugin/.apm"
+cat > "$FIXTURE7/.claude-plugin/marketplace.json" <<'JSON'
+{
+  "name": "test-marketplace",
+  "plugins": [
+    { "name": "apm-plugin", "source": "./plugins/apm-plugin" }
+  ]
+}
+JSON
+cat > "$FIXTURE7/plugins/apm-plugin/.claude-plugin/plugin.json" <<'JSON'
+{
+  "name": "apm-plugin",
+  "skills": ["./skills/does-not-exist"]
+}
+JSON
+if bash "$SCRIPT" "$FIXTURE7" > /dev/null 2>&1; then
+  pass "an apm-native plugin (has .apm/) is not checked here, even with a broken pointer field"
+else
+  fail "check-manifests.sh failed on an apm-native plugin -- pointer-field validation should be delegated, not duplicated"
+fi
+
 echo ""
 echo "Results: $PASS passed, $FAIL failed"
 [[ $FAIL -eq 0 ]]