What I did is after untarring the CMSMS install files, I created a file called .htaccess in the /cmsmadesimple-1.2.3/install/ directory, with the following contents:
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AuthName "Installdir"
AuthType Basic
AuthUserFile /home/mydir/installprotection/.htpasswd
Require valid-user
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htpasswd username
Now, whenever I copy the install files to make a new website, the install dir is always password protected, disallowing the public or the nefarious from messing up my installs/upgrades.
This probably seems like really basic stuff to some of you, but others may find it helpful. It's a simple thing you can do to be more secure.