How to reorganize drupal sites/all/modules structure without symbolic links? Context:

As the number of modules used increases, I try to reorganize modules in /***/sites/all 
into 


sites/all/modules/contrib 
sites/all/modules/custom
sites/all/modules/dev


subfolders as it is described here (1) and now I use a solution similar to what was answered here (2)

Question: 
Is possible to use path variable or another solution instead of creating symlinks for each contrib module?

I don't want to create so many symbolic links for each of contrib modules separately. 

How to explain to Drupal the sites/all/modules structure the way I don't get bootstrap.inc errors such as:

Error: require_once(): Failed opening required
'/***/sites/all/modules/entity/includes/entity.inc'
(include_path='.:/usr/local/php5/lib/php') in
/***/includes/bootstrap.inc, line 2935
The Registry Rebuild module really is the answer. I struggled to solve this problem for hours, then this module fixed it completely, and with elegance!