1. The plain text conversion is really meant to define a plain text ebook format using lightweight markup (specifically markdown). So that you can create plain txt files with links and headers and formatting and lists and even tables. It is not meant to "do the right thing" with every text file you throw at it. That's not going to change as I prefer to run dedicated tools on a txt file from a given source (e.g. gutenmark) and then convert the HTML.
2. Are the multifile conversion still causing crashes? I though I'd squashed that bug a while ago.
3. Making the displayed columns customizable is on my TODO list
4. In version 0.3.34 you'll be able to search for the term !lrf to get a list of books that dont have an LRF format (this is not a 100% safe since the search will be over all metadata so some book that has the string "lrf" in its metadata wont show up, but this is the best you'll get until i implement an advanced search dialog.
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