I'm interested in keeping my project's classes, triggers, etc. in custom folders, but I cannot, since this data is currently stored in the .sfproj file.  This is OK if the team is using a version control system (VCS), but even in that case it can still problematic for two reasons:

1. Login credentials are also stored in the .sfproj file, preventing me from committing it to (VCS)
2. If I create a NEW project within Welkin Suite, the folder structure is not preserved - I have to build it again any time I create a new project.

The two above problems make custom project structure useless to me as a developer because I work on a team, and we do not currently use a versioning system (I'm fighting that battle right now, but currently that's the way it is).  This is unfortunate, because custom project structure is an AWESOME feature!

I propose that TWS start storing custom project structure data in a custom metadata type (see here).  Custom metadata type records are themselves stored as metadata, making it ideal for this use-case.  E.g. a custom metadata type could include a field for file-path, file-type, and last-modified time (last modified of the custom path, not of the file itself).  Welkin Suite could then retrieve and update these custom object type records as part of its regular push/pull action.  Any files which do not have an entry in the custom metadata type would be placed in Welkin Suite's default locations.

• https://welkinsuite.com/using-custom-salesforce-project-structure-to-improve-productivity/
• https://developer.salesforce.com/blogs/engineering/2015/04/custom-metadata-types-ga.html