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This also happens when doing other things, like setting the encoding programmatically makes the buffer dirty, even though it didn't change anything...

You can easily do this yourselves by creating a file type specific setting that overrides the indentation style.
Only one request per submission. Please split it up.
I completely agree, the current implementation is very annoying.

Some additional things:

- It should only show icon and filename as default, as illustrated by OP.

- If you press for example Option when viewing the list it should expand to show the full path, with the path grey and the filename still black:
I keep them in my Dropbox and symlink them into the Sublime folder.