[Here's the above question in a slightly more readable format...]

I'm trying to write a cron job that periodically, automatically deletes all the cookies that I don't want. But Firefox seems to store cookies outside of the sqlite database that is supposedly used for that.

To illustrate:

~/.mozilla/firefox/XXXXXXXX.default $ rm cookies.sqlite* # delete all cookies.sqlite files

~/.mozilla/firefox/XXXXXXXX.default $ ps aux | grep fire # make sure firefox isn't running anymore

name 20593 0.0 0.0 14228 1092 pts/5 S+ 23:24 0:00 grep --color=auto fire # it's not

~/.mozilla/firefox/XXXXXXXX.default $ sqlite3 cookies.sqlite  # open the cookies database

SQLite version 3.11.0 2016-02-15 17:29:24

Enter ".help" for usage hints.

sqlite> select * from moz_cookies;

Error: no such table: moz_cookies # it doesn't exist.

Leave sqlite. Start Firefox.

~/.mozilla/firefox/XXXXXXXX.default $ sqlite3 cookies.sqlite 

SQLite version 3.11.0 2016-02-15 17:29:24

Enter ".help" for usage hints.

sqlite> .tables

moz_cookies # cookies.sqlite / moz_cookies exists again

sqlite> select count(*) from moz_cookies; # and it contains 2 cookies

2

But in Firefox, when I now select Preferences > Privacy > Remove individual cookies, I get a much larger list of cookes. Where are they stored, if not in the cookies.sqlite database?

You would first have to tell what cookies this is about.

Note that Firefox stores the cookies from the current session in sessionstore.js, so if you restore that session on the next start then you automatically will get the cookies from the previous session that were saved.

• http://kb.mozillazine.org/browser.sessionstore.privacy_level

There are also some special (persistent) cookies that are used by specific services that may or may not be stored in cookies.sqlite, but are kept in local storage or IndexedDB.