Using Update Scripts

Every time I use the update scripts (manually download from Wiki and running the scripts via putty) they run a module update which will download and install all modules even though I have ether uninstalled, disabled, and/or removed modules we are not using.

Is there a way to set ether the script or a status in the module where it will only update modules that are installed and active?

I am running FreePBX 11, 12 and 13 and it seems to happen on all of them.

Modules that are disabled should not be affected by the upgrade script.

Ok, I will check to make sure they are disabled in my next run of updates.

Is there a way to prevent new modules from installing?

After they install the first time, disable.