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'the "Applications" subdirectory of the Mathematica base directory' is a standard location for add-ons. That directory is included in the default list of directories to look in for add-ons (the "$Path" variable). I don't understand your second...
I think you will have to state your question more clearly. What was the application that you were installing? Did you unzip it directly into the \$UserBaseDirectory/Applications folder or \$BaseDirectory/Applications folder? You may have it at the...