diff --git a/install.sh b/install.sh
index 8c9da89..81c3a8d 100755
--- a/install.sh
+++ b/install.sh
@@ -108,14 +108,16 @@ install_claude() {
   fi
 
   # commands/rules/skills/agents — skip files that already exist (don't overwrite custom ones)
+  # Handles both flat *.md files and subdirectory-based skills (e.g. skills/research/SKILL.md)
   for dir in commands rules skills agents; do
-    for f in "$DOTFILES_DIR/claude/$dir/"*.md; do
-      [ -f "$f" ] || continue
-      dest=~/.claude/$dir/$(basename "$f")
+    for f in "$DOTFILES_DIR/claude/$dir/"*.md "$DOTFILES_DIR/claude/$dir/"*/; do
+      [ -e "$f" ] || continue
+      name=$(basename "${f%/}")
+      dest=~/.claude/$dir/$name
       if [ -e "$dest" ] && [ ! -L "$dest" ]; then
-        echo "    Skipped $dir/$(basename "$f") — already exists (not overwriting)"
+        echo "    Skipped $dir/$name — already exists (not overwriting)"
       else
-        lns "$f" "$dest"
+        lns "${f%/}" "$dest"
       fi
     done
   done