Great insights into your Idea Factory. Have you considered any of the emerging class of visual note-taking tools? They are much more flexible for atomizing ideas and concepts and enabling you to create random "collisions" between them - the basis of serendipity! I've been writing about these tools for some time. Here are 5 examples:

MILANOTE: https://mindmappingsoftwareblog.com/milanote-review/

COPPICE: https://mindmappingsoftwareblog.com/coppice-app-interview/

SPEARE: https://mindmappingsoftwareblog.com/speare-idea-processor-review/

SCRINTAL: https://mindmappingsoftwareblog.com/scrintal-review/

NAPKIN: https://mindmappingsoftwareblog.com/napkin-interview/