Hi Tomas,

i'm answering off the top of my head, so bear with me in case
this is not entirely accurate, i'm lacking the time to check the
details right now.

> I installed jre-1.7.0 from packages and add directories to
> /etc/man.conf, but when using 'man -k' I can see some messed output.

What apropos(1) = man -k gives you comes from the whatis database,
see makewhatis(8) and weekly(8).  Now /usr/libexec/makewhatis is
a Perl script parsing installed manual pages, in a rather clever
way, trying to extract the information needed by apropos(1).

Sometimes, it is astounding what kind of fancy stuff people put
into man pages, making it very hard for makewhatis(8) to make head
or tail of it.  That *may* be the problem here.  To make sure,
one would need to look at the man pages in question and at the
code in /usr/libexec/makewhatis (read it!) and figure out what's
happening.

> Is it correct output for those man pages or is is something broken in
> my /etc/man.conf ?

Very probably, man.conf(5) is not the problem.

> $ man -k java
> Java IDL: Transient Naming Service (1) - \f2tnameserv
> This (1) - document discusses using the Java IDL Transient Naming

Might be strangely formatted manual(s) confusing makewhatis(8)...

Yours,
  Ingo

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