Break up the Makefile into a header, footer and a user customizable body which drives the configuration of the build.  This helps to hide some of the nastiness of the rules which isn’t that important to the average developer.  Support more than one C file and more than one assembly file and link it all together.  Put the disk image into a template file and change the rule to copy and modify it as necessary.  Add a Virtual ][ machine to the repository which will (eventually) be launched by the Applescript rather than just using the top window in the app.
Add support for all the machine config types.  Generate include file dependencies and load them into the makefile so .h file changes causes the right files to rebuild.  Rework the applescript a bit to load a specific virtual ][ machine and reboot into that machine on launch.  Add a DOS 3.3 template disk for the DOS 3.3 machine config types.
Some final fixes to handle the fact that the header is not there consistently.  So, we need to validate that the first two bytes in the binary is the expected start address and if so, then there is a header which needs to be stripped.