Grand juries are secret by law. Nobody involved is allowed to talk about what happens in the grand jury, or even to acknowledge the subject of the investigation.
That seems very very wrong.
Manning is in jail because she has a different idea of right and wrong than the judge does. That wouldn’t matter at a cocktail party, but in this case the judge has the power to punish Manning until she changes her mind about what the honorable thing to do is.
There is no judge present in a grand jury hearing. The only reason Manning was in front of a judge was that her lawyers argued that the prosecutor was using the grand jury incorrectly. Since Assange has already been indicted, there isn’t much sense in collecting additional evidence from Manning.
To be honest, that argument sounds plausible to me. The judge rejected it, and ordered Manning to testify or be held in contempt. Sadly, since the news reports generally ignore Manning’s legal arguments, they also ignore the details of the judge’s order.
I can think of a couple of possibilities: (1) Assange isn’t the only target (I think this is unlikely, but possible), (2) the prosecutor intends to file additional charges against Assange (I think this would be likely in a case without extradition, but extradition complicates things), (3) Manning’s lawyers are simply wrong about the limits on grand juries, or (4) the prosecutor may well be doing something wrong, but the judge can always fix it after the fact and Manning is obligated to play along for now. I really would like to know why Manning’s request was denied. All I can say right now is that she’s in contempt because she refuses to testify in front of the grand jury knowing that she won’t be charged with any more crimes related to the matter and knowing that Assange has already been charged.
This reasoning does not make sense. The bar for indictment is not "100% of all available evidence must have been collected". One can and should collect (and subsequently present) additional evidence until the closing arguments are presented. No case is ever a "sure thing". One is wise to continue to reinforce it throughout the entire process.
“According to [a spokesperson], Manning’s lawyers maintain that, since the grand jury is only an investigative tool and cannot be used by prosecutors to prepare for trials, the subpoena for Manning ‘represents an improper and impermissible use of the grand jury process.’”
Apparently the judge disagreed with that argument, but I can’t find any reports on the judge’s reasoning.
There's no secret court involved. But, yes, grand jury proceedings are secret to protect the integrity of the system as an honest probable cause filter for serious charges, which is an important public check on government and protection of the potentially accused.