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Total noob here, just loaded Ubuntu 12.04 for the first time yesterday. Loaded Cinnamon desktop also, to try out both it and Unity.

I downloaded an application SMathStudio.exe into my Home/Downloads folder, unzipped it, made it work on mono in Cinnamon by right-clicking. So far so good.

But where should I keep it, what's the Linux philosophy? I tried to drag and drop it into /usr/bin but couldn't, can't drag and drop without root privelege. It just fails, doesn't even ask for your password.

So opened a terminal and "sudo cp"-ed it into /usr/bin. Except now that it's there I can't run it, can't double click it, can't add a shortcut to the Cinnamon menu as "sudo mono SMathStudio.exe" fails, opens a terminal and gives heaps of error messages.

So what's the general principle of where applications should live, and how you should access them in Cinnamon?

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There's no hard and fast rule for this. Generally you can put things like that in ~/bin, add it to your path if you want it from the command-line, and add a .desktop file in /usr/share/applications if you want it in Unity.

At least for me:
If it's in /bin implies linux standard.
If it's in /usr/bin it implies distribution standard.
If it's in /usr/local/bin it implies a one-off of distribution standard or something you did yourself that you want accessible to all users.

That being said, if you want it run-able by all users you need to sudo chmod +x random.exe it.

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One major consideration that differentiates executables in /bin from those in /usr/bin is this: /usr must be able to be a separate partition, or even a network share (and the same /usr/bin could be shared between many workstations). Binaries that have to be available when just / is mounted, or available to access NFS in the first place, or must be accessible for single user mode to be usable, are located in /bin or /sbin and not in any subdirectory of /usr. It is in this sense that binaries in /bin and /sbin are "essential" in ways that others are not. –  Eliah Kagan Jul 22 '12 at 3:34
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