Inksky
If you sideload books onto your Kindle regularly, you have probably run into three problems sooner or later: the Kindle fills up with junk folders you cannot see, your highlights file becomes an unreadable mess, and half your sideloaded books show up without covers. Here are three free tools that solve each of these problems, and none of them require jailbreaking.
1. SDR Cleaner — Remove Orphaned Sidecar Folders
Every time you sideload a book, Kindle creates a companion .sdr folder next to the file. These folders store your reading position, bookmarks, highlights, and annotations. When you delete a book from the Kindle’s own interface, the .sdr folder gets cleaned up too. But when you delete a book by just removing the file over USB — or when Calibre removes a book during a library sync — the .sdr folder stays behind.
Over time, these orphaned folders pile up. I checked mine after a year of sideloading and found over 600 orphaned .sdr folders eating up nearly 200MB. That is space you cannot use for actual books, and it slows down the Kindle’s indexing.
SDR Cleaner is a tiny open-source utility that scans your Kindle’s documents folder over USB and removes every .sdr folder that no longer has a matching book file. It is safe — it only deletes sidecar folders where the parent ebook has already been removed. You connect your Kindle via USB, point SDR Cleaner at the mounted drive, and it does the rest in seconds.
Download from the SDR Cleaner GitHub releases page. Works on Windows, macOS, and Linux. No installation needed — just extract and run.
2. Clippings Fere — Format Your My Clippings.txt
Kindle stores every highlight and note you make in a single file called My Clippings.txt in the documents folder. Open it and you will see why people built tools around it: every clipping is dumped in chronological order with no grouping by book, no formatting, and lots of repeated metadata lines.
==========
The Name of the Wind (Patrick Rothfuss)
- Your Highlight on page 247 | location 3758-3759 | Added on Tuesday, 15 March 2025 21:43:11
It was the patient, cut-flower sound of a man who is waiting to die.
==========Multiply that by two hundred highlights and you have a file that is borderline unusable.
Clippings Fere is a desktop tool that parses My Clippings.txt and outputs something you can actually work with. It groups highlights by book, strips out the repetitive metadata, and lets you export to Markdown, plain text, or CSV. I use it to turn my Kindle highlights into reading notes for book club discussions — no more copy-pasting from a wall of equals signs.
Download Clippings Fere from clippings.io or use the free Clippings Converter tool. Both do the same core job: turn Kindle’s raw clipping dump into organized, exportable notes.
3. Cover Fixer — Fix Missing Book Covers
Nothing bugs me more than opening my Kindle library and seeing a row of blank cover thumbnails with just title text. This happens when you sideload a book whose EPUB file has a missing or malformed cover image, or when Calibre does not embed the cover properly during conversion.
The fix is simpler than you might think. Plug your Kindle into your computer, then use Calibre to polish the book: right-click the title in your Calibre library, select Edit metadata → Download cover, pick a cover, then use Polish books (or Embed metadata) to force Calibre to embed the cover into the file. Resend the book to your Kindle and the cover appears.
For bulk fixes, Calibre’s Polish books feature can process multiple books at once, embedding covers and updating metadata in batch. If a book still refuses to show its cover, try converting it from EPUB to EPUB — this forces Calibre to rebuild the file with the cover image embedded in the correct place. Then delete the original from your Kindle and send the converted version.
These three tools together take maybe ten minutes to run and will keep your Kindle library clean, organized, and pleasant to browse. I run SDR Cleaner about once a month and check covers whenever I sideload a batch of books.