Can anyone tell me what this little clover-esque icon overlay means in the project list window? I take it to mean a file-specific option has been changed, but I can't work out what it is.
Your assumption is correct. See also: https://developer.arm.com/documentation/101407/0538/Creating-Applications/Project-Targets-and-File-Groups/File--Group--and-Component-Attribute-IconsAll the 'Options for File" tabs have a 'Default' button. If you press it, you should see the modified option appear or disappear.