For an add-on to work the file structure hast to be like this:
Code:
AddOns/
└── MyAddOn/
├── MyAddOn.txt
└── other_files_or_folders
If the manifest file doesn't have the same name as the folder then the other files (lua etc.) aren't loaded (update, see EDIT). However it will still be visible in-game under ADD-ONS, even with the specified metadata if available. This applies to all txt files in the MyAddOn folder (not for subfolders).
In my opinion it would be better if only the txt file with the same name as the folder would be used and all other txt files ignored. That way it would also be possible to have a README.txt or similar in the folder.
The other option would be to allow all txt files in the folder and also include the listed files of all the txt files.
The way it currently is just doesn't make much sense in my opinion and is only confusing.
EDIT:
Files listed inside of any txt file (located in AddOns/*/) are loaded, but the path is relative to the file name (more info
this post).