I wouldn't continue to try and bodge together your current build. Start again. Somewhere along the way something has gone horribly wrong. You're missing (lots of) vital files.
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I find that in my install (from source) the /opt/zimbra/conf contain only one file (dspam.conf) and only one directory (spamassassin)
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As you point out, you're missing most of the conf directory. Virtually nothing (including ldap) will work without this. Copying stuff in from a binary install is *NOT* a fix.
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./zmdumpenv: line 36: /opt/zimbra/libexec/get_plat_tag.sh: No such file or directory
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rpm: To install rpm packages on Debian systems, use alien. See README.Debian.
error: cannot open Name index using db3 - No such file or directory (2)
package zimbra-core is not installed
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get_plat_tag.sh is so fundamental to the building and running of zimbra, if you don't have this in place give up and go home. this is the reason you're getting the alien/debian message above, by default the zimbra installers drop down to rpm if it doesn't find another platform defined.
how are you installing the end zimbra? are you doing a make inside ZimbraBuild? do you end up with ZimbraBuild/zcs-<version>? and then do a install.sh from inside there? my instructions:
Ubuntu Hardy - Build Zimbra
are not complete, they have never been released to the public yet. some of the instructions rely on build script patches from solaris source that I removed from the ubuntu patch I submitted for cleanliness. they are 98%, I'll try and finish them soon.