If you'd prefer that all your books are consolidated in one folder, you can use the free ebook tool Calibre to modify a MOBI file's Personal Doc settings before you sideload it to your device. Here's how to do so:
- Launch Calibre, and then load the MOBI file to your library via the "Add books" button at the top left of the navigation bar.
- Select the book from the title list and click "Convert books" from the top nav bar. Make sure at top that "Mobi" is selected in both the "Input format" and "Output format" dropdowns.
- A Convert dialog box will open. Click "MOBI Output" in the lefthand pane.
- In the "Mobi file type" dropdown, choose "both" to ensure compatibility with both newer and older Kindle devices. In the "Personal Doc tag" field, change "[PDOC]" to "[EBOK]" (this controls the destination directory on the Kindle). See below.
- Click OK, and Calibre will convert and output a fresh MOBI. Sideload this to the Kindle as usual, and it should show up in the Books list instead of the Docs list on your device.
Warning: In my own testing on v0.9.23 of Calibre for OS X, during the MOBI-to-MOBI conversion process, Calibre stripped out the existing CSS in the MOBI document. By default, it also will modify the formatting of the Table of Contents. You can use the Extra CSS field under Look & Feel in the Convert dialog box and the settings under Table of Contents to adjust CSS and TOC configuration, respectively, but if you are concerned about faithfully preserving MOBI formatting, you may want to forgo using Calibre to change the Personal Doc settings altogether at this time.
For more information on tweaking the Personal Doc settings in MOBI, as well as more geeky discussion of the structure of the EXTH header that contains the relevant metadata, you may want check out these discussions on the MobileRead forums, which I referred to when investigating this issue*:
As well as the MobileRead Wiki documentation on the MOBI format.
You may also want to check out a couple other tools for modifying the Personal Doc settings: the Java Mobi Metadata Editor, which provides a simple GUI for modifying the metadata in a MOBI's header file, and the Mobiperl toolset, which lets you do the same with command-line Perl scripts. I experimented tweaking the Personal Doc settings with both of these tools on KF8 files, but was not able to produce MOBIs that would go into the Books folder instead of the Docs folder. It appears that additional metadata modifications may be necessary for KF8, but this is still being investigated; see the discussion on MobileRead on this topic.
* Unfortunately, because MOBI is a proprietary standard, most of the knowledge captured on the MobileRead forums and Wiki is based on analysis and reverse engineering by ebook developers, rather than formal spec documents.