I've been organizing my personal collection of ebooks (epubs & pdfs) lately so I've been thinking of possible "best practices" to employ and wanted to open a discussion on it.

There are sources for free ebooks online which are trustworthy such as https://archive.org/index.php and https://www.gutenberg.org/ which provide DRM-Free copies in multiple formats.

These are great but a few of my ebooks are from less trusted sources so handling the security aspects should be considered as well. (Example: An interesting PDF from Hacker News or Reddit)

General:
For general organization and management, Calibre (https://calibre-ebook.com/) has been very useful so far. You can use Calibre to handle converting, meta-data, reading, and organization of your library.

Security:
From what I can research the epub and pdf formats can be both vulnerable to malicious but the potential is much higher for pdf. As you then might expect, pdf exploits are more common.

A few precautions you can take include using your browsers pdf viewer versus a standalone alternative, using an up to date and secure pdf reading with JavaScript disabled, or relying on a cloud service such as google drive that allows online viewing.

An offline e-reader is another easy solution as the malicious code would require a much more specific attack vector.

Reading:
https://us.norton.com/internetsecurity-emerging-threats-is-it-safe-to-download-free-ebooks-online.html
https://www.baldurbjarnason.com/notes/epub-javascript-security/

Mine are a bit of a mess, with decades of accumulation and lack of maintenance resulting in a forest of poorly organized folders and completely inconsistent filename schemes.

I'm interested in hearing about things like folder hierarchies/taxonomies, naming conventions, and techniques for efficient access. This goes for everything from personal documents to projects to pictures to media collections.