diff --git a/.megamemory/knowledge.db b/.megamemory/knowledge.db
new file mode 100644
index 0000000..0a06b00
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diff --git a/.megamemory/knowledge.db-shm b/.megamemory/knowledge.db-shm
new file mode 100644
index 0000000..24376d4
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diff --git a/.megamemory/knowledge.db-wal b/.megamemory/knowledge.db-wal
new file mode 100644
index 0000000..af8d9fe
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diff --git a/setup.py b/setup.py
index 7441f8e..12ba739 100644
--- a/setup.py
+++ b/setup.py
@@ -454,7 +454,9 @@ def get_category_for_skill(skill_name: str) -> str:
     exact_match = False
     if skill_name.startswith('"') and skill_name.endswith('"'):
         exact_match = True
-        name_lower = skill_name[1:-1].strip().lower().replace("_", "-").replace(" ", "-")
+        name_lower = (
+            skill_name[1:-1].strip().lower().replace("_", "-").replace(" ", "-")
+        )
     else:
         name_lower = skill_name.lower().replace("_", "-")
 
@@ -523,9 +525,12 @@ def migrate_skills():
 
         dest = cat_dir / folder.name
         if dest.exists():
-            shutil.rmtree(dest)
+            if dest.is_symlink() or dest.is_file():
+                dest.unlink()
+            else:
+                shutil.rmtree(dest)
 
-        shutil.move(str(folder), str(cat_dir))
+        shutil.move(str(folder), str(dest))
 
         category_counts[category] = category_counts.get(category, 0) + 1
         moved_count += 1
@@ -625,9 +630,26 @@ def generate_pointers(category_counts):
 
 def main():
     import argparse
-    parser = argparse.ArgumentParser(description="SkillPointer Setup - Infinite Context. Zero Token Tax.")
-    parser.add_argument("--agent", choices=["opencode", "claude"], default="opencode", 
-                        help="Target AI agent (opencode or claude)")
+
+    parser = argparse.ArgumentParser(
+        description="SkillPointer Setup - Infinite Context. Zero Token Tax."
+    )
+    parser.add_argument(
+        "--agent",
+        choices=["opencode", "claude"],
+        default="opencode",
+        help="Target AI agent (opencode or claude)",
+    )
+    parser.add_argument(
+        "--skill-dir",
+        type=str,
+        help="Directory to search for skills (overrides --agent default)",
+    )
+    parser.add_argument(
+        "--vault-dir",
+        type=str,
+        help="Directory to move skills to when creating pointers (overrides --agent default)",
+    )
     args, unknown = parser.parse_known_args()
 
     if args.agent == "claude":
@@ -635,6 +657,11 @@ def main():
         CONFIG["active_skills_dir"] = Path.home() / ".claude" / "skills"
         CONFIG["hidden_library_dir"] = Path.home() / ".skillpointer-vault"
 
+    if args.skill_dir:
+        CONFIG["active_skills_dir"] = Path(args.skill_dir).expanduser().resolve()
+    if args.vault_dir:
+        CONFIG["hidden_library_dir"] = Path(args.vault_dir).expanduser().resolve()
+
     # Handle 'install' argument for compatibility with Install.bat/vbs
     if unknown and unknown[0] == "install":
         pass