Placed files in consistent locations for all core modules:

all .js files in modules placed in a /js/ directory
all .tpl.php files in modules placed in a /templates/ directory
all .tests.info files in modules placed into the /tests/ directory
all .*.inc files in modules placed into the module root directory

all .admin.inc files in modules placed into the module root directory
all .pages.inc files in modules placed into the module root directory
all .theme.inc files in modules placed into the module root directory

views_ui module moved outside views module (to match field and field_ui)

Introduced in branch: 
1.0.x
Introduced in version: 
1.0.0
Impacts: 
Module developers
Theme developers
Related Github Issues: 
https://github.com/backdrop/backdrop-issues/issues/486