Need help on 'Merge directory' for upgrading

Looking at your cp command, that should have been

In other words, "copy recursively everything in the modx-2.3.5-pl directory to this directory". What you were telling it to do was to copy to the server's root directory, not to your web root.

If you put the install.php file in the web root (www or htdocs or public_html), and select the 2.3.5 Traditional installation, it will put everything you need in the web root.

Hmm. No, it won't. It does disappear the core directory if it's a standard installation to begin with. Use the master branch version, then. https://github.com/sottwell/installer

The advanced-upgrade branch's version does work for "hardened" installations where the core is not in the web root. Obviously this needs some work.

Ok. Version 1.6.1 fixes that bug. And it was a pretty stupid bug, too.

Thanks all. I have gave up on upgrading. I just restored the file back from the back up.
I did try using SSH as sottwell suggested. It asked me to overwrite million of files.