[boreq]

That is the exact problem that the standard I talk about was designed to solve (apart from the clutter in the home directory).

[wool_gather]

I think saagarjha's point was that an even simpler standard would be for the creating application to use file metadata to annotate the files. And a simpler standard is generally more likely to be followed, especially if it's unilateral.

This doesn't help with installation, obviously, but it helps with cleanup.

[masklinn]

The classic MacOS had exactly this concept: Creator Code[0], similar to the Type Code[1] but storing a file's creator rather than its "mimetype".

[0] https://en.wikipedia.org/wiki/Creator_code

[1] https://en.wikipedia.org/wiki/Type_code

[wool_gather]

Good point, I had almost forgotten about those!