diff --git a/scripts/bootstrap.py b/scripts/bootstrap.py
index 505295b..cf354b4 100644
--- a/scripts/bootstrap.py
+++ b/scripts/bootstrap.py
@@ -722,18 +722,36 @@ def main() -> int:
                 print(f"  ✗ Error testing 'mm': {e}")
         else:
             # POSIX (Linux/macOS)
-            user_bin = home / ".local" / "bin"
-            mm_sh = user_bin / "mm"
+            # Check likely installation locations
+            locations = [home / ".local" / "bin" / "mm", Path("/usr/local/bin/mm"), Path("/usr/bin/mm")]
+            found_shims = [p for p in locations if p.exists()]
             
-            print(f"Checking for shim file:")
-            print(f"  mm: {'✓' if mm_sh.exists() else '✗'} ({mm_sh})")
+            print(f"Checking for shim files:")
+            for p in locations:
+                if p.exists():
+                    print(f"  mm: ✓ ({p})")
+                else:
+                    if args.debug:
+                        print(f"  mm: ✗ ({p})")
+            
+            if not found_shims:
+                print(f"  mm: ✗ (No shim found in standard locations)")
             print()
             
             path = os.environ.get("PATH", "")
-            user_bin_str = str(user_bin)
-            in_path = user_bin_str in path
+            
+            # Find which 'mm' is actually being run
+            actual_mm = shutil.which("mm")
             print(f"Checking PATH environment variable:")
-            print(f"  {user_bin_str} in current session PATH: {'✓' if in_path else '✗'}")
+            if actual_mm:
+                print(f"  'mm' resolved to: {actual_mm}")
+                # Check if it's in a directory on the PATH
+                if any(str(Path(actual_mm).parent) in p for p in path.split(os.pathsep)):
+                    print(f"  Command is accessible via current session PATH: ✓")
+                else:
+                    print(f"  Command is found but directory may not be in current PATH: ⚠️")
+            else:
+                print(f"  'mm' not found in current session PATH: ✗")
             print()
             
             # Test if mm command works
@@ -1205,14 +1223,33 @@ if (Test-Path (Join-Path $repo 'CLI.py')) {
 
                 else:
                     # POSIX
-                    user_bin = Path(
-                        os.environ.get("XDG_BIN_HOME",
-                                       str(home / ".local/bin"))
-                    )
+                    # If running as root (id 0), prefer /usr/bin or /usr/local/bin which are standard on PATH
+                    if os.getuid() == 0:
+                        user_bin = Path("/usr/local/bin")
+                        if not os.access(user_bin, os.W_OK):
+                            user_bin = Path("/usr/bin")
+                    else:
+                        user_bin = Path(os.environ.get("XDG_BIN_HOME", str(home / ".local/bin")))
+                    
                     user_bin.mkdir(parents=True, exist_ok=True)
 
                     mm_sh = user_bin / "mm"
                     
+                    # Search PATH/standard locations for existing 'mm' shims to avoid conflicts
+                    common_paths = [user_bin, Path("/usr/local/bin"), Path("/usr/bin"), home / ".local" / "bin"]
+                    for p_dir in common_paths:
+                        p_mm = p_dir / "mm"
+                        if p_mm.exists() and p_mm.resolve() != mm_sh.resolve():
+                            try:
+                                # Only remove if it looks like one of our shims
+                                content = p_mm.read_text(encoding="utf-8", errors="ignore")
+                                if "Medeia" in content or "Medios" in content or "cli_entry" in content:
+                                    p_mm.unlink()
+                                    if not args.quiet:
+                                        print(f"Removed conflicting old shim: {p_mm}")
+                            except Exception:
+                                pass
+
                     # Remove old launcher to overwrite with new one
                     if mm_sh.exists():
                         try: