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.