For a simple script cleaning:

1. Click open, choose save game file.
2. Click FixInstances, its removes all orphan script instances.
3. In left list, scripts that starts at "#->" select one and click a Delete script.

When you have removed them, click Save button -> overwrite.. -> yes (only if u have backup)
Load a save in game, and save it again. Now it should be fully cleaned.


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Other:

 Clean havok moved:
  removes all items forms that are moved by game physics or magic, shouts etc.


Scripts:

 List active:
  Shows currently active script instance names.

 Inc.refs:
  Removes forms linked on selected script instances, when you remove that script.
  Dont use it, unless you know what forms here is.


Plugins:

 Del mod forms:
  Removes all selected plugins forms from save. Can be used for reset some plugin its default state.
 
 Forms:
  Delete, save or load saved form.

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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 treated as 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) type is 0, and they are filtered out of list.

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





