As far as your terminal not opening, I'm not sure I understand exactly what you did. What is the script exactly? Where are you running the script? If you are using a launcher, I believe the program can be running in a shell but a terminal window does not open. I'm not in GNOME right now (I'm loving using i3WM), but I'm remembering right, when you make a launcher there is a checkbox asking if you want the process to run in a shell.
It's totally normal that your home directory is NOT in your path. Your home
directory is not where you are supposed to put binary files (or other
executables). That is why you create a bin directory. When you type in a
command to execute a file, all of the directories in your path are checked
until the executable file is found. If you store lots of things in your home
folder--like most people do--such as Videos and Music and Documents, those
will be searched unnecessarily. Make sense?
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