I want the "X-Spam-Flag:" header to show either "yes" or "no" for spam resp. no-spam labeled emails, in all emails labeled as spam, there should be a full report in the email-header with the words that Spam Assassin reacted upon. In the present state Spam Assassin doesn't really label the emails at all. I'm adding the contents of my local.cf-file below. Note that with 2.6x, this local.cf configuration labeled all incoming emails as wanted.
if it labeled them all with a X-Spam-Flag header it was a bug..
add_header spam Flag _YESNO_
Right there you're explicitly telling it to only add a X-Spam-Flag header to spam, and therefore, not add it to nonspam.
I suspect you want this instead:
add_header all Flag _YESNO_
auto_learn 1
replace that with bayes_auto_learn.
always_add_headers 1 spam_level_stars 1 use_terse_report 1 report_header 1 detailed_phrase_score 1
defang_mime 1
Please obliterate the above lines, they are all no longer valid. You've got some very outdated options there... detailed_phrase_score became deprecated with the release of version 2.50!
And be sure to run spamassassin --lint sometime, so you can see SA complain about all the invalid options in your configfiles!
rewrite_subject 0 subject_tag
These two have been replaced with rewrite_header. See the UPGRADE docs: http://svn.apache.org/repos/asf/spamassassin/branches/3.0/UPGRADE