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When the pbimageviewer application was first written by Michail Polubisok, it was only for reading image files found in directories. The directory chooser was used to select which directory to read the images from. Afterwards, I added support for archive files (CBZ,...). Since the archives are files rather than directories, you can't use the directory chooser to select them. Rather, you have to modify extensions.cfg and go through the Library tab to choose archives. Because of the way that PocketBook devices work, you need the two different ways of handling directories and files.
This isn't 100% true. You can use pbimageviewer as the default viewer for images by adding entries for them to the extensions.cfg file, and thus could do without the copy in /applications, but it doesn't hurt to have the option of opening directories available.
I copy files over WiFi using scp after installing the sshd service on the readers. It saves me effort on plugging/unplugging the USB cable repeatedly while testing. I understand, though, that scp isn't convenient for most people. It's possible to set up Filezilla to access the reader via sftp instead, which provides a nice GUI for those who prefer it.
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