`dms setup` should not remove comments from config files

### Feature Description

Please update `dms setup` commands so that they keep comments in config files.

### Use Case

_No response_

### Compositor(s)

All compositors

### If Other, please specify

_No response_

### Proposed Solution

_No response_

### Alternatives/Existing Solutions

_No response_

Find the entry point for the `dms setup` commands and follow how they read and write config files. Reproduce the setup flow with comments in a config file, then verify that the completed setup preserves those comments across all compositors.

Written by the indexing model from the issue text.