I have this one semi open source Windows application (HeidiSQL) that can't be compiled to a Linux executable because it uses a proprietary build system. Unfortunately, the native alternatives all really suck. So I installed Wine. With the default Wine settings, Wine injects the following files in my ~/.local/share/applications directory:

wine-extension-chm.desktop
wine-extension-gif.desktop
wine-extension-hlp.desktop
wine-extension-htm.desktop
wine-extension-html.desktop
wine-extension-ini.desktop
wine-extension-jfif.desktop
wine-extension-jpe.desktop
wine-extension-msp.desktop
wine-extension-pdf.desktop
wine-extension-png.desktop
wine-extension-rtf.desktop
wine-extension-txt.desktop
wine-extension-url.desktop
wine-extension-vbs.desktop
wine-extension-wri.desktop
wine-extension-xml.desktop

There are many general file types rebound to Wine's alien apps, causing my native environment to open text files in notepad instead of gedit, for example. I consider this highly impudent, so I deleted the desktop files. So far it seems fine.

I wouldn't consider it impudent when installing a native app. Swapping a native app with another is fine. Wine is alien though and IMHO shouldn't register its apps by default.

It is debatable whether this should be reported upstream (https://bugs.winehq.org/show_bug.cgi?id=19182) and/or also reported here. From Wine POV, they are replacing the environment with some of their own bits, why wouldn't they want to do it? But from the native POV, a stranger is invading the environment with non-integrating apps, why would you want to have that? I understand I can disable the behaviour, but the damage is done for every new Wine user.