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1) I'd like to get rid of the Y! local
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That's just a zimlet you can disable in your default class of service.
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2) Change the Yahoo web search box at the top of the screen, to search our company
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Removing the box entirely is supported; search these forums for "evil yahoo search." Save the screen width for the email search box, especially on laptops.
To add company search, do a zimlet or make a search provider plugin for the search box already present in all current web browsers anyway.
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3) AJAX/HTML interface titlebar text. And Zimbra logo from the top-left.
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The "free" license prohibits changing these, but they're easy to change in any of the supported editions. Resist the temptation to change much, because you'll regret it at every software update. Logos can be replaced in the _base skin.
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4) Auth our shared files Samba server, proFTPd FTP server, Apache intranet server with Zimbra LDAP.
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All trivial except the samba server, because microsoft protocols require microsoft-encrypted passwords (registry hacks to allow plaintext are possible, but a bad idea). Several ways to crack this nut: 1) There exist unsupported tools for extending zimbra ldap schema to provide posix and samba users. Search the zimlet gallery and zimbra blog. 2) You could go the other way, making samba-ldap (or apple opendirectory, or ms ad) your authoritative password store, and cross-authenticate zimbra against that. 3) Maintain accounts & passwords separately, but have people set/change passwords via a web page that talks to both systems.
Or, depending on what you use it for: Drop the samba server entirely. Use the WebDAV protocol to access Notebook/Briefcase files on the zimbra server instead.