WordPress Template Heirarchy

Greetings!

I am planning to create a well organized file organization system in my wordpress theming. My approach was to group related files into sub folders.

Example:

Instead of having taxonomies template under

/wp-content
    /your_theme_name/
       taxonomy-your_custom_taxonomy.php
       taxonomy2-another_custom_taxonomy.php
       taxonomy3-yet_another_custom_taxonomy.php

I will going to group this into

/wp-content
    /your_theme_name
       taxonomies/
            taxonomy-your_custom_taxonomy.php
            taxonomy2-another_custom_taxonomy.php
            taxonomy3-yet_another_custom_taxonomy.php
       custom_post_types/
            //custom post type files, etc.

Base on this link,
WordPress has already a Template Heirarchy and I am currently following that style.

However, sometimes I feel that my files are not well-organized and I need to move related files into sub folders ( for taxonomies, post types, specific author page,etc ).

Does wordpress allow this or does wordpress has already built-in API for this? Or Do I need to reinvent the wheel.

Thanks in advance! ??