Jennifer
Take a snapshot, reboot and take another snapshot. That'll be what you need to ignore when you reboot
generally speaking, you are asking a $1Million question, as what needs to be removed involves a huge amount of skill, judgement and experience. Here are some pointers:
1) Look for things that are machine specific, usernames, SIDs, database names, network paths, IP addresses or things that were requested at installtime.
All those things need to be turned into Properties
2) Things that are always safe to remove are temporary data. Their names are generally a giveaway: MRU, bag, bucket, cache, last, temp, etc.
Most log files too are safe to ignore.
3) Try to use Repackager's Monitor mode as it (when it works) gives far cleaner results by watching the changes that are made by the installation, ignoring those made by Windows.
4) Maintain a central exclusions list on one of the servers and only give the supervisor (yourself) write access to default.ini. If everyone runs repackager from this central location then you should get consistant results.
5) Read
this book. looeee