Mod Organizer (MO) supports the use of Profiles. For more info see the Profiles tab of the MO wiki. All profiles are stored in the directory
A profile is a a directory with a set of text-files and optionally contains save games. The saves directory inside
The following text-files exist for a profile. Not all of have to exist.
- initweaks.ini. Automatically generated. Doesn't have to exist. Read by the game. This file is local 8-bit encoded
- lockedorder.txt. Generated from the UI. Doesn't have to exist. This file is utf-8 encoded
- archives.txt. List of bsa's that should be registered (as in: loaded through the ini). Ideally this would list all bsas in active mods. This list is one entry per line, sorted by priority (as in: files from the second bsa overwrite those from the first, third overwrites first and second, ...). Filenames are including extension but without path, i.e. "Skyrim - Voices.bsa". This file is utf-8 encoded
- modlist.txt. List of mods and whether they are enabled in the profile or not. One mod per line. Name only (no path). Every line starts with a plus (enabled) or minus (disabled). The order here is the inverted order the files appear in the UI (the first mod in the file is the last in the UI -> highest priority). This file is utf-8 encoded.
- loadorder.txt. Lists all plugins (esm, esp, both active and inactive) by load order. One plugin per line. This file is used and generated by boss. This file is utf-8 encoded
- plugins.txt. List of enabled plugins (esm, esp) ordered by load order. One plugin per line. This file is also accessed by boss and read by the game. This file is local 8-bit encoded
- skyrim.ini. Game settings. Regular game settings format. This file is local 8-bit encoded
- kyrimprefs.ini. Regular game settings format. This file is local 8-bit encoded
Note: Modlist.txt contains all installed mods (whether active or inactive) for a profile. If a mod is added in the current profile the modlist.txt for the other profiles is not updated, not even when MO is restarted. When switching to another profile the modlist.txt is updated with the new mod(s).
Tannin stated: Please note: If I'm not mistaken MO will not recognize externally generated profiles until it is restarted.