In the "user preferences" (I am guessing the name since I do have a Polish menu) I have selected "Scan only a Books folder in flash memory" (guessing a name again). Then I moved all my books to "Books" folder. I have reconfigured Calibre to export to "Books". I have cleared the cache of Pocket, FeedMe to get rid of the html files. After restart it indexed my books only. I have run Pocket and Feedly again so that their cache is populated again. After another restart unfortunately it again was looking for metadata in html files
. The good thing is that after that change I don't have html files in the Library anymore. So it still scans the html files from time to time but the Library stays clean.