I originally started programming on a Borland IDE, which allowed me to place my projects files into a tree that was independent of their layout on disk.

I became so attached to it, I helped reimplement similar functionality for SciTE (scitepm).  

(I'm not sure whether the attached picture will show up, but it illustrates how I like to group, say the 'cloud' functionality together in a web project, even though the elements of that functionality lie in 'templates', ' static/js', 'static/css', etc)

However, apparently SciTE isn't being updated in my distribution (Fedora), and it would be better to have this functionality embedded in something with forward motion - like Geany.

The functions that this would include are : 
a)  Do a search upwards from the current directory for a suitable '.geany/tree-project.conf' 
b)  Load a tree of files from some YAML-like format on disk, and put them in a side-bar tab
c)  Allow this tree to be edited (new sub-groups, add a file, delete a file, etc)
d)  Save tree to disk (typically this wouldn't change much once a project had stabilised - so the file could be put in git, for instance).  This wouldn't include 'currently open' indicators, since they're more volatile.
e)  That's about it : Other tools look like they're already doing a great job for file searching, etc.

If this already exists, please let me know : I don't want to reinvent the wheel.

All the Best
Martin
:-)

PS:  tree-browser in current git looks like a good launching-off point, structure-wise