On the Pentagon’s new military commission website, a clerk has scrawled "secret" in place of a convict’s photo in the court record, documents handed out to reporters a year ago are excluded, and unclassified court documents are missing.

The website was unveiled last month to rehabilitate the reputation of the Guantánamo war court. So far, it’s hodgepodge of secrecy — and still a work in progress, according to Defense Department officials, while clerks, lawyers and the intelligence community haggle behind the scenes over what the public can see.

It’s been more than a year in the making and the Pentagon has yet to reveal its cost. Every screen bears the slogan “fairness, transparency, justice.”

But a review of the content has found that it pointedly leaves out some of the key controversies that have bedeviled the war crimes trials, from allegations of torture to a comparison of the Seminoles to al Qaida.

Moreover, the clerk of the court still has not developed a standard for the hybrid court that borrows from military and civilian justice systems.

A case in point: Most photographs of detainees and children already shown in open court are shielded from the public. But dig around and you can find the passport pictures of Osama bin Laden’s kids and alleged 9/11 mastermind Khalid Sheik Mohammed.

Obama appointees at the Defense Department committed to create the new website more than a year ago after attorneys and executives for McClatchy and other news organizations protested secrecy and ad-hoc rule making at the military trials.

Reporters working under crude conditions at Guantánamo’s Camp Justice had complained for years that clerks and judges unfamiliar with the federal system were inconsistently releasing documents. But the urgency of improving transparency increased after the Pentagon briefly banned four reporters from covering war crimes trials in the summer of 2010 in a dispute over ground rules. As part of talks that led to new ground rules, senior Pentagon officials also agreed to add the website.

But whether the web site will accomplish media hopes of timely transparency is anything but certain.

A new, still undisclosed regulation gives the war court clerk three weeks to consult intelligence agencies on what to make public, according to Pentagon sources familiar with the secret rule-making. Under that timeline, motions filed days ahead of hearings might still be argued at the court without the public seeing their contents.

The Pentagon’s former Bush-era detention czar, Naval Reserve Cmdr. Cully Stimson, a military judge, called the new website “not perfect” and far from complete.

But he labeled it “long overdue” and a “monumental improvement over the status quo” in a blog posting at the Conservative Heritage Foundation.

“Time will tell whether it can provide real-time documents for pending cases,” he added.

Confessed war criminal Omar Khadr, now 25, could go home to a Canadian lockup later this month to serve out at most seven more years of an eight-year sentence. Notes from the diplomatic agreement are available on the war court website.

But still under suitability review a year after they were presented in court are a photo used by prosecutors that showed Khadr as a child in traditional garb at mine-making class in Afghanistan — and a Danish psychologist’s article called “Muslim Inbreeding: Impacts on intelligence, sanity, health and society.”