Document run command line tools with flatpak

Command-Line.md

@@ -129,6 +129,15 @@ file or set the `$PATH` variable in your `.profile` or `.bashrc` file.
 If Barrier has been installed using a package manager or equivalent it should
 already be in your `$PATH`.
 
+If installed using flatpak, you can run the command line client like this:
+```cmd
+flatpak run --command=barrierc com.github.debauchee.barrier
+```
+And server like this:
+```cmd
+flatpak run --command=barriers com.github.debauchee.barrier
+```
+
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