ConfigFile directives in .inf-files

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I'm (still :) trying to fully automate ldap installation for our specific
deployment with setup-ds.pl in silent mode.. I have an inf which uses
ConfigFile directives to try to define indexes, cache sizes and other
settings for the directory server. My problem is, only a small part of those
ConfigFiles are applied when I check dse.ldif after, but no errors anywhere.
I tried using --debug but the only output I could see of relevance was:
"+Processing config.ldif ..."
"+Processing indexes.ldif ..."

NONE of the settings in the ConfigFile make it to dse.ldif except
"nsslapd-dbcachesize" and "nsslapd-cachememsize".. These are both set
properly, or I would doubt if the files had been processed at all. But the
the replication manager isn't created and size/timelimits are not set and so
on, and the same with indexes. I can see nothing in the output log from the
script and there's nothing in the logs for the newly created server.

If I instead add the ConfigFiles with ldapmodify, things work fine.

My guess is I'm trying to modify attributes that don't exist yet? The Red
Hat documentation at
http://www.redhat.com/docs/manuals/dir-server/install/8.0/Installation_Guide-Advanced_Configuration-Silent.htmlseems
to indicate that I should be able to create a replication manager, but
the difference I can tell from the docs is that their RM is made in the
directory itself while I'm trying to use the cn=config database.

Here's a snippet from my config.ldif:

# doesnt get created
dn: cn=replication manager,cn=config
changetype: add
objectClass: inetorgperson
objectClass: person
objectClass: top
cn: replication manager
sn: RM
userPassword: password
passwordExpirationTime: 20380119031407Z

# is set properly
dn: cn=config,cn=ldbm database,cn=plugins,cn=config
changetype: modify
replace: nsslapd-dbcachesize
nsslapd-dbcachesize: 512000000

# is not set
dn: cn=default instance config,cn=chaining database,cn=plugins,cn=config
changetype: modify
replace: nsslapd-sizelimit
nsslapd-sizelimit: 20000
-
replace: nsslapd-timelimit
nsslapd-timelimit: 120

# is set
dn: cn=userRoot,cn=ldbm database,cn=plugins,cn=config
changetype: modify
replace: nsslapd-cachememsize
nsslapd-cachememsize: 512000000
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