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In addition to the locations that kiloseven has listed, you can also find installed apps in /usr/share/applications. Another way to Open With is to right click on the desired file, and choose Open With, and then pick the application or choose Other Application, and click on Show other applications, and browse for more. See images below.
An URL consists of not only an address, but also of a protocol. The latter is what the apps directory uses to open the Software Center. The link on the Gnome Schedule page points to apt://gnome-schedule. Your browser has been instructed to redirect apt:// links to the Software Center. In technical terms, the Software Center has been registered as a protocol ...
That's right, for there's no single place to put an app in Linux. There's no monolithic One Way To Do Things in Linux, no mandate from above, and the well-written guidelines (e.g., http://www.tldp.org/HOWTO/HighQuality-Apps-HOWTO/fhs.html which explain why take some time to find and read. /bin, /usr/bin, /sbin, /usr/sbin, /usr/local, /usr/local/bin, ...
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