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@jackie_w: Turn off automatic metadata update under calibre integration in the preferences and the file will not be touched unless you do a save. last_modified is not intended to track file time modification, tweak book is no different in that respect. Currently, tweak book operates completely independently of calibre, you can close calibre and TB will continue to work. Changing it to update last modified dates will mean that will change. Not a tradeoff I think is worth making.
I prefer having the current element at the top of the panel, as having it at the center means you can never be sure exactly where it is and your eyes have to scan around looking for it. Also showing the element at the center is not very robust. It works for simple layouts, but more complex ones can cause problems with the element not perfectly positioned. Showing it at the top uses the browsers' own implementation and is much more robust.
The Files Browser does not track the currently opened file. You can select multiple entries in the files browser, so having it track the current file doesn't make much sense. I suppose I could it have it show the currently opened file in bold, but the selected files are not going to change.
Re: colors: I'll have a look at increasing the contrast in wombat for selected text and nbsp highlighting. In any case, at some point I will add the ability to create your own custom themes, then you can tweak the colors to your hearts content.
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