diff --git a/install-plugins.sh b/install-plugins.sh
index d9028b6..e8eef12 100644
--- a/install-plugins.sh
+++ b/install-plugins.sh
@@ -659,6 +659,11 @@ NPX_SKILLS=(
   "alchaincyf/find-skills"
 )
 
+# `skills add` resolves its target (.agents/skills/, skills-lock.json) RELATIVE
+# TO THE CWD. Running it from the repo (which carries gitignored .agents/ and
+# .claude/ dirs) makes skills land in $REPO/.agents/skills instead of
+# $HOME/.agents/skills — where link.sh expects them — and the bug is
+# self-reinforcing once $REPO/.agents exists. Always install from $HOME.
 if ! command -v npx &>/dev/null; then
   warn "npx not available — skipping external skills"
 else
@@ -669,18 +674,28 @@ else
       ok "$_name already installed ($_dst)"
       continue
     fi
-    info "Installing $_name via: npx -y skills add $_src"
-    if npx -y skills add "$_src" 2>/dev/null; then
+    info "Installing $_name via: npx -y skills add $_src (from \$HOME)"
+    if (cd "$HOME" && npx -y skills add "$_src" 2>/dev/null); then
       if [ -d "$_dst" ]; then
         ok "$_name installed"
       else
         warn "$_name installed but not at expected path $_dst"
       fi
     else
-      err "$_name install failed — run manually: npx -y skills add $_src"
+      err "$_name install failed — run manually: (cd \"\$HOME\" && npx -y skills add $_src)"
     fi
   done
 fi
+
+# Earlier runs (before this CWD fix) scattered skills into the repo's gitignored
+# .agents/skills and .claude/skills. They shadow the canonical $HOME copies and
+# confuse skill discovery — remove them. Both are gitignored, so this is safe.
+for _stray in "$REPO/.agents/skills" "$REPO/.claude/skills"; do
+  if [ -d "$_stray" ]; then
+    rm -rf "$_stray"
+    info "Removed stray repo-local skills dir: $_stray"
+  fi
+done
 echo ""
 
 # ============================================================
@@ -790,6 +805,23 @@ if [ "$ADDED" -eq 1 ]; then
 fi
 echo ""
 
+# ============================================================
+# STEP 10 — REFRESH SYMLINKS (final, so this script is self-sufficient)
+# ============================================================
+# Steps 2/8/8.5 INSTALL skills (gstack submodule, emil/frontend/motion, npx
+# darwin/find-skills) that link.sh must symlink into ~/.claude/skills/. Since
+# link.sh runs BEFORE this script in install.sh, those symlinks would be missing
+# on a fresh run until link.sh is run again by hand. Re-run it here so
+# `make plugin` (and `make install`) finish complete — nothing left to do.
+echo "── Step 10: Refreshing symlinks (link.sh) ─────────────────"
+echo ""
+if [ -f "$REPO/link.sh" ]; then
+  bash "$REPO/link.sh"
+else
+  warn "link.sh not found — run it manually to create skill symlinks"
+fi
+echo ""
+
 # ============================================================
 # SUMMARY
 # ============================================================
diff --git a/update-all.sh b/update-all.sh
index 373568c..28fbc84 100644
--- a/update-all.sh
+++ b/update-all.sh
@@ -287,10 +287,13 @@ if command -v npx &>/dev/null; then
     fi
     # `skills add` is idempotent and pulls latest from the source repo,
     # which is the closest thing to an update operation the CLI exposes.
-    if npx -y skills add "$_src" 2>/dev/null; then
+    # Run from $HOME: the CLI resolves .agents/skills/ relative to the CWD, so
+    # running from the repo would write into $REPO/.agents/skills (gitignored)
+    # instead of $HOME/.agents/skills where link.sh expects it.
+    if (cd "$HOME" && npx -y skills add "$_src" 2>/dev/null); then
       ok "$_name refreshed from $_src"
     else
-      warn "$_name refresh failed — run manually: npx -y skills add $_src"
+      warn "$_name refresh failed — run manually: (cd \"\$HOME\" && npx -y skills add $_src)"
     fi
   done
 else