They are in all of those! :P It would probably help to know that this is following the "Filesystem Hierarchy Standard" (here it is on Wikipedia). It helps when one can easily get a list of installed files via the package manager, but the application manager here does not appear to have a GUI for that...
Linux Directory Structure The directory structure of Linux/other Unix-like systems is very intimidating for the new user, especially if he/she is migrating from Windows. In Windows, almost all programs install their files (all files) in the directory named: `Program Files.’ Such is not the case in Linux. The directory system categorises all installed files. All configuration files are in /etc, all binary files are in /bin or /usr/bin or /usr/local/bin. Here is the entire directory structure along with what they contain...