Calibre is a somewhat popular eBook management package that's also free software. <http://calibre-ebook.com/>
Install via
# apt-get install calibre
There is a somewhat unfortunate interaction between Calibre and git-annex...
* git-annex makes its files become read-only. By the way, that's not quite obvious from the documentation; I suggest making that more prominent.
* Calibre modifies files (not quite sure of semantics, how, or why) when doing various operations, notably such as when copying a book from one's library to one's portable reading device.
These don't play well together, sadly.
I'd expect most of the issue to sit on the Calibre side, and have reported it as a bug.
Preliminary indication is that they're treating it as a functionality change they'll decline to fix. Which isn't entirely unreasonable - I anticipated as much, and I don't want to treat that as a bad/wrong decision.
However, I think it's:
* Unfortunate, as fitting Calibre together with git-annex seems like a neat idea.
* Useful to make sure that this kind of "doesn't play well together" condition is documented, even if only as a bug report.