Skyrim Special Edition
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This external tool is an exe you can use to reduce the number of saves present in your MO2 saves folders. It will remove up to half of the saves for the selected character in the selected MO2 profile. It always saves the most recent 10 saves and the first 5 saves for that character. It will delete every other save between those saves.

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This tool allows you to reduce the number of saves present in your Mod Organizer 2 (MO2) saves folders. You must select the profile and character for which you wish to manage saves. You should run this tool every time you think you have too many saves on a character. In the tool, character names will be followed by the GMT +0 time and date that the first save of that character in that saves folder was made.

New in 1.1.0: Now you can also choose the Default Saves checkbox and point it at the "Documents\My Games\Skyrim Special Edition\saves" folder (the default Skyrim SE save location). 

When you first run the program a settings file will be generated in the same folder as the exe. This allows the program to save your Mod Organizer\Skyrim SE folder location, and Documents\My Games\Skyrim Special Edition\saves folder location as well as your last run profile and character, for convenience.

Example: There are 100 saves for the character named Prisoner Bob. When you use this program, it will not delete saves 1-5 or saves 91-100. It will delete every other save between those saves, so save 6, 8, 10, 12, 14, [and so on] 84, 86, 88, and 90.

This effectively reduces the number of saves by half while preserving important saves and not just deleting the bottom half of your save list.

This tool was written in python (source in misc downloads) and compiled into an .exe using pyinstaller (spec file in misc downloads). Just in case you'd rather compile for yourself.

The UI isn't perfect so some things might look weird, but it does Just Work. See the mod images for a preview.

Other notes: it is possible to have save files which end with .tmp or .bak in your saves folder. This program does not do anything to those files. It will ignore them. However, it will delete .skse save files that do not have a corresponding .ess save file (these are orphaned skse cosaves).

Disclaimer: Since this is a custom-built application, some anti-viruses may flag it as harmful. I can't change that, but if you wish to verify how/what the tool does, the source file is posted in the optional downloads.