make heavy changes to makefile

- clean when makefile changes (ang generate compile_commands.json)
- better handling for directory dependencies
- reorganise code more
- add dependency tracking so it triggers recompiles on header file changes

.vscode/tasks.json

@@ -48,14 +48,6 @@
                 "isDefault": false
             },
             "detail": "builds the program for web using emscripten"
-        },
-        {
-            "label": "create compile_commands.json",
-            "type": "shell",
-            "command": "bear -- make",
-            "runOptions": {
-                "runOn": "folderOpen"
-            }
         }
     ]
 }