If you use metadata editor and make many changes, those changes are recorded to the mdr.btd and mdr.idx files.
The problem is that these files endlessly grow as you make changes to your models (note plural).
This is because the files are appended to only.
This is a request to allow the ability to compact the files.
Currently the way to go about cleaning things up (some customers complain of > 5 minutes to save their model) is:
1) Export all models to XMI files.
2) Stop metadata editor.
3) Delete the mdr.btf and mdr.btx files
4) Open the metadata editor and import the xmi files.
This creates a new index file for the metadata editor and can resolve some performance issues.