Hrm... weird enough, this is what my strace tells me (a symlink from
/etc/my.cnf to /etc/mysql/my.cnf exists):

$ strace mysqldump 2>&1 | grep my.cnf
stat64("/etc/my.cnf", {st_mode=S_IFREG|0644, st_size=3959, ...}) = 0
open("/etc/my.cnf", O_RDONLY)           = 3
stat64("/home/tkeller/.my.cnf", 0xbf8ccdb4) = -1 ENOENT (No such file or 
directory)
stat64("/usr/local/Zend/Core/etc/my.cnf", 0xbf8ccdb4) = -1 ENOENT (No such file 
or directory)

I have no idea why it looks for /usr/local/Zend/... (this directory path
doesn't exist entirely), but if you say it works for you, its probably
some weird local issue.

-- 
mysqldump doesn't pick up /etc/mysql/my.cnf
https://bugs.launchpad.net/bugs/342578
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