I did #1, no problems.
#2, it repaired a bunch of permissions. There was one warning about a missing SUID file. I googled it and it looks like that was not a problem. I ran repair again and everything was fine.
#3:
System Launch Agents: (What does this mean?)
[loaded] com.apple.SafariNotificationAgent.plist
- Executable not found!
System Launch Daemons: (What does this mean?)
[loaded] com.apple.HeadlessStartup.plist
- No signature!
[running] com.apple.collabauthd.plist
- Executable not found!
[running] com.apple.collabcored1.plist
- No signature!
[running] com.apple.collabcored2.plist
- No signature!
[running] com.apple.collabcored3.plist
- No signature!
[running] com.apple.collabcored4.plist
- No signature!
[loaded] com.apple.collabd.expire.plist
- No signature!
[running] com.apple.collabd.notifications.plist
- No signature!
[running] com.apple.collabd.plist
- No signature!
[loaded] com.apple.collabd.quicklook.plist
- No signature!
[running] com.apple.collabfeedd.plist
- No signature!
[running] com.apple.collabsandboxd.plist
- No signature!
[loaded] com.apple.devicemanager.plist
- No signature!
[loaded] com.apple.diskspacemonitor.plist
- No signature!
[loaded] com.apple.mail_migration.plist
- No signature!
[loaded] com.apple.opendirectorybackup.plist
- No signature!
[loaded] com.apple.passwordreset.plist
- No signature!
[loaded] com.apple.pcast[redacted]d.plist
- No signature!
[loaded] com.apple.salearn.plist
- No signature!
[loaded] com.apple.updatesa.plist
- No signature!
[loaded] org.apache.htcacheclean.plist
[Click for support]
[loaded] org.calendar[redacted].calendarserver.plist
[Click for support]
[loaded] org.clamav.clamd.plist
[Click for support]
[failed] org.clamav.freshclam-init.plist
[Click for support] [Click for details]
[loaded] org.clamav.freshclam.plist
[Click for support]
[loaded] org.dovecot.dovecotd.plist
[Click for support]
[loaded] org.dovecot.fts.update.plist
[Click for support]
[running] org.jabber.jabberd.plist
[Click for support]
[loaded] org.jabber.jabberd_notification.plist
[Click for support]
[running] org.jabber.proxy65.plist
[Click for support]
[loaded] org.list.mailmanctl.plist
[Click for support]
[running] org.postgresql.postgres.plist
[Click for support]
Later:
User Launch Agents: (What does this mean?)
[failed] com.apple.CSConfigDotMacCert-[...]
@me.com-SharedServices.Agent.plist
[Click for details]