Manafort is going to plead guilty in the second trial. The agreement is not yet out, but there is a new superceding "information" filing, which apparently is like an indictment but only used for cases that don't require a grand jury indictment or when the defendant has agreed to plead guilty (see the Cohen guilty plea).
The filing apparently has a ton of documentary evidence, which from what I'm reading is extraordinarily rare. Speculation is that they're doing this so that any pardon will be seen as what it is: a CYA by Trump, since it lays out explicitly how effing guilty Manafort is. It also does still include forfeiture of a lot of his property. Whether or not he's cooperating remains to be seen.