In case that you antivirus doesn't like a file: It seems like antiviruses often gives a false alarms for files written on certain tools/programming languages, and that seems to happen for this tool. So, it's possible, that your antivirus program goes mad, when you downloaded this.
This program is created using RosAsm, so source is included in .exe file. Available in misc files too. Be free to edit it as you wish.
How to use it?
1. Click open, choose a save game file.
2. Click "FixScriptInstances", it removes all orphan script instances.
3. This is optional, and not compatible with all mods. Click a Delete all #
4. Push save or save as button. Make sure you have backups for both savename.ess and savename.skse (if its installed). Load a save in the game, and save it again. Now it should be fully cleaned. Re-saving removes script names etc.
Auto backup, if on,(default) creates a backup from your save, named as backup-date-time.ess and backup-date-time.skse. In versions 2.00< only savename.ess backup is created.
"Clean other" this cleans orphan array7 items + visited worldspace array items having a formId 0. "Clean formlists" removes all form lists items with refId 0.
Dont use "Inc.refs", unless you know what forms it deletes!
Game crashes when saving a cleaned save? Here's how awjnash got it to work: Another thing you can try, if saving a game crashes, is to click a 'del. broken actives' button after you cleaned orphan scripts.
Thanks to CHABAL
For versions 1.00 - 1.13 Thanks to LiveStyleGaming
Information used when creating this tool: http://www.uesp.net/wiki/Tes5Mod:Save_File_Format