You should store all of your Java source files in the src directory, or subdirectories within the src directory.
You should store any graphics files (e.g. .jpg) or other non source-code resources in the resources directory, or subdirectories within the src directory.
For convenience we've supplied some execution scripts that will compile/run code with the --add-modules flag set (for Java FX). Use javac.sh to compile on Linux and Mac OS, or javac.bat to compile on Windows. Likewise, use java.sh to run on Linux and Mac OS, or java.bat to run on Windows. E.g.
$ cd comp16412-coursework-1_username
$ ./javac.sh src/MazeApplication.java
$ ./java.sh MazeApplication
Note that in the above example, on line 3, the name of the class file to run (MazeApplication) is NOT prefixed with the source path.
We've supplied a shell file, run_tests.sh, that should work on Linux/Mac OS.
The file run_tests.bat should do the same thing on Windows. This file is purely for your convenience and (a) won't be used in marking, (b) isn't something we're going to provide lots of support for!