Tucson, Arizona (CNN) -- A federal judge Wednesday entered "not guilty" pleas on behalf of Jared Lee Loughner, the Arizona man accused of fatally shooting six people and wounding 13 others, including U.S. Rep. Gabrielle Giffords.
Judge Larry Burns also scheduled a May 25 competency hearing for Loughner, and attorneys on both sides will be allowed to hire their own experts to evaluate Loughner's competency to stand trial.
Prosecutors sought the competency hearing, saying that Loughner had believed the FBI was bugging him, had extreme animosity toward the government, and was even hearing voices.
Loughner's public defenders didn't want such a hearing, saying it would be premature and could interfere with their ability to develop a relationship with Loughner.
But the judge said his review of materials relating to Loughner left him concerned.
"We can't do anything until I'm assured that Mr. Loughner is on board and able to assist" in his own defense, the judge ruled.
Last Thursday, a federal grand jury returned a new indictment against Loughner in which he is charged on 49 counts -- including murder and attempted murder -- related to the shooting outside a Tucson supermarket in January.
Loughner, 22, entered the courtroom with a slight grin, the first time he's appeared in a Tucson courtroom. His bald head is now showing growing hair.
When a clerk asked if his name was Jared Lee Loughner, he responded: "Yes, it is."
The judge entered the "not guilty" pleas for Loughner at his attorneys' request. Loughner waived the reading of all 49 charges against him.
In response to motions, the judge ordered prosecutors to release grand jury materials to the defense, but said Loughner's attorneys cannot reproduce the documents or leave copies with Loughner.
Burns also ordered the release of findings from authorities' search of Loughner's parents' home in Tucson, as requested by two Arizona media outlets. Last month, the judge sided with prosecutors in withholding the information because the investigation was ongoing and a grand jury was still preparing an indictment.
But with a new indictment now issued, the judge said it is time to unseal the documents relating to what was found in the Loughner family home.
"The active investigation is over," the judge said. "Ninety percent of the information in the warrant domain is already in the public light."
He added, "There is something mystic and suspicious in not releasing this type of information."
Burns said he will delay ruling on a motion filed by prosecutors Monday to force Loughner to submit a handwriting sample -- a request that he, thus far, has refused.
The government wants the sample to compare with handwritten notes found in Loughner's residence that include mentions of Giffords "as well as references to guns and bullets," according to a court document. It says he has resisted such requests to date, "arguing that the court lacks authority" to force him to provide a sample.
"There being no other avenue to obtain the defendant's handwriting exemplar, the government now seeks an order to compel," prosecutors wrote in the motion.
Burns said he wants to discuss some material collected by bureau of prisons on Loughner since he was arrested.
Prosecutors said they want the court to review the materials, to see if they should be able to see it. But Loughner's public defenders said they want time to review the matter and prepare arguments in writing.
As the hearing unfolded and the judge made his decisions, Loughner sat still.
The full courtroom included about 20 family members of victims and seven people supporting Loughner, including a woman who dabbed her eyes with tissue.
Among the spectators were Bill Badger, one of two men who jumped on Loughner and subdued him during the shooting, and shooting victim Susan Hileman. Also attending was Mavy Stoddard, who was wounded in the attack and whose husband, Dorwan, a retired construction worker, died trying to shield his wife from the bullets.
Loughner's family members declined to comment as they left the courthouse.
Tucson attorney Michael Piccarreta, who appeared in court on behalf of slain federal Judge John Roll and his family, was asked by reporters afterward what he thought of seeing Loughner face-to-face.
Responded Piccarreta: "He's just another defendant."
Loughner was earlier indicted on three counts of attempted murder, including one alleging that he tried to kill Giffords with a Glock semiautomatic handgun during the event she was hosting for constituents.
Giffords, who was shot in the head, is undergoing rehabilitation at a medical facility in Houston.
The new indictment supersedes the earlier one. It adds murder charges connected to the deaths of Roll, a federal district judge, and Gabriel M. Zimmerman, a staff member for Giffords.
Loughner also faces charges in the deaths of Dorothy J. Morris, Phyllis C. Schneck, Dorwan C. Stoddard, and a child, referred to in the indictment as C-T G. Nine-year-old Christina-Taylor Green was among those killed in the shooting.
Autopsy reports released Monday showed that Zimmerman, Schneck and Stoddard suffered fatal head wounds, while the three others were shot in the chest.
If convicted, Loughner could face a death sentence, U.S. Attorney Dennis Burke said last week, although prosecutors have not said whether they will seek the death penalty.
CNN's Ted Rowlands reported from Tucson and Michael Martinez contributed from Los Angeles.