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Replicating the same icon on every file of the same type is redundant. It also makes it impossible to use the current emblems for indicating covers/opf/ncx files etc. In other words, it restricts the functionality of the files browser to cause less confusion for people that expect it to reflect a folder structure. I could certainly remove the indents, but then that will run counter to how every tree structure in every application works, potentially confusing far more people.
These are expectations that have built up over years of using Sigil. Just give it time, those expectations will dissolve. There is always some friction when migrating between similar but somewhat different software. That is inevitable.
One of my principles is to not restrict edit book to conform to UI expectations from Sigil, that is a long term losing proposition. Because once you choose a particular UI changing it in the future carries very high migration costs for software as popular as calibre.
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