Save cleaner V 1.13 beta. This tool is open source, you can use it and its ideas for your own projects as you wish.


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FOR A BASIC SCRIPT CLEANING:

1. Click open, choose a save game file.

2. Click a "Fix all #->" button to remove all scripts, that are detected as orphan.
   It can take a while if there is lots of them.

3. Click "FixScriptInstances", it removes all orphan script instances.

   (Script instances, that aren't linked on any object, those usually comes,
    when a mod creates a copy from some vanilla item, who have script attached.
    Instaces are then left on a save, if that mod is later removed.)

4. Push Save button -> overwrite.. -> yes (only if you have a backup)
   Load a save in 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 Savenamexx.ess-backup.ess


Other way:
 If you want to keep some scripts, that auto detection is marked as orphans, (ones begin at #->)
 just choose a script you want to remove and click a "Delete script".

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OTHER BUTTONS:

Scripts:

 List active:
  Shows currently active script instance names. (or stack names, because usually lists a same name many times, i'm not sure, quite few documentation about it)
  It can crash this tool on some saves. (v1.13 added more infos and fixed one bug.)

 Inc.refs:
  Removes forms linked on selected script instances, when you remove that script. Does nothing on orphan script instances.
  Be careful with it, if there is, say 00000014 id in some instance, it removes your player..

 dbg:
   Show what instances was removed, when "FixScriptInstances" button was clicked.


Misc:

 Reset havok: (usually quite useless)
  Removes all items forms, that are moved by game physics or magic, shouts etc.


Plugins:

 Delete mod forms: ( eg. have installed dungeon mod, killed all creatures on it, and want play it again. Otherwise quite useless)
  Removes all selected plugins forms from save. Can be used for reset some plugin its default state.


Forms:

  Delete, save or load a saved form. Can be used to tranfer things between different saves.


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Information used:
 http://www.uesp.net/wiki/Tes5Mod:Save_File_Format


Orphan instance detection (FixScriptInstances) works as if script instance RefId is 0, instance is orphan.

 http://www.uesp.net/wiki/Tes5Mod:Save_File_Format/Papyrus#ScriptInstance
 0 RefId instances seems to be not present on saves that are used without uninstalling a mod.


Orphan script detection works as if script type is 0, script is orphan one and marked as #->.
 Some vanilla scripts (3 of them: Alias, ActiveMagicEffect and Form) type is always 0, and they are filtered out of orphan list.

 http://www.uesp.net/wiki/Tes5Mod:Save_File_Format/Papyrus#Script