As @Nicole Aaron mentioned, there is no officially proposed folder structure for your InterSystems project, but I can share one typical approach.
The upper folder is basically named "src" assuming source code inside.
Files inside "src" could be splitted by source type. E.g.:
"cls" - for ObjectScript classes,
"inc" - for include files,
"mac" - for mac routines,
"dfi" - for DeepSee dashboards and pivots.
Every class name consists of package(s) and class itself. So class package could be projected to a folder. E.g. source code for the class Sample.Person will be stored in the file with following path:
There are numerous projects on Github which use similar approach. You can find examples of such projects via these cacheobjectscript-udl tag, e.g. this project.