more backporting of real world project Justfile changes to template

[joshuadavidthomas]

• Remove module name from --cov CLI flag for pytest-cov and allow it to read the config for what modules to cover
• Shorten coverage commands in py module
• Remove test command as prereq for coverage commands; this seems like a good idea (always ensure the test command runs) but ends up doubling up running the test suite, depending on the order they are called.
• Remove refresh command as it has too much overlap with update
• Ensure shell command enters the app container if dj is passed