CAIRO Mohamed Fawzy was just 21 when he was jailed by an Egyptian military court for 25 years, accused of stealing refrigerators.
"Since his arrest last year, I have been exhausted and hysterical," said his mother Sabreya Fahmy, choking back tears. "I could kneel at the president's feet to bring me back my innocent son."
At least 12,000 civilians have gone before army courts in the security vacuum that followed the fall of Egyptian leader Hosni Mubarak, according to the campaign group No to Military Trials, and at least 5,000 are still in jail.
Many of those jailed were arrested in the protests that erupted during the 18 months an interim military government was in charge in Egypt, and some have even been tried since civilian President Mohamed Mursi took office in June.
Mursi has pardoned 630 civilians on the recommendation of a committee he formed to study the cases of 2,165 prisoners. The committee said the cases of the remaining prisoners needed to be investigated further.
Activists want the remainder to be released or at least referred to civilian courts for retrials. Until Mursi acts, they say, his claim to champion the cause of last year's Arab Spring uprising will be open to question.
"It is shameful that President Mursi, who rose to power because of these civilians' struggle and the time they are spending in jail, is sitting in his palace eating with his family, while we have no clue what has become of the people inside those prisons," said prominent activist Ahmed Domma.
They also say the situation is a direct - and dangerous - challenge to Mursi, Egypt's first elected head of state in 5,000 years. Mursi earlier this month dismissed the country's top generals in a bold show of power after 60 years of military leadership.
"The military is still continuing to sentence people and use military tribunals as if it is saying to the president you are not the only one in power," said Salma Abdel-Gelil, a member of No to Military Trials.
Activists have long complained that military trials were used by Mubarak to secure convictions that might not have been possible in more open and accountable civilian courts.
A QUESTION OF PRIORITIES
Mursi and the Muslim Brotherhood, the socially conservative movement from which he hails, came late to the uprising against Mubarak that was begun by liberal and left-wing activists.
While voicing the same commitment to democracy as those of revolutionaries, and pressing the army to stick to its timetable for elections, the Brotherhood generally avoided direct confrontation with the generals when they were temporarily in charge.
To its critics, the Brotherhood has shown more dedication to the pursuit of power than to human rights and the rule of law.
"The track record of the Brothers during this period is characterized by promises broken and silence in the face of abuses, such as military trials for civilians and the application of the emergency law for most of the SCAF's tenure," Michael Wahid Hanna of The Century Foundation wrote in Foreign Policy, referring to the Supreme Council of the Armed Forces.
"The Brothers, in tandem with the SCAF, also sought to tarnish those intent on continuing the protest movement through mass mobilization and public actions," he said.
Mubarak's overthrow and the election of Mursi has transformed Egypt's stale politics. But many Egyptians say the unreformed security forces still disregard the basic rights of citizens.
Activists say the use of torture by security officials is still common, though officials in the past have routinely denied such practices are routine and say any allegations of torture are properly investigated.
"WE WERE LUCKY"
Karim El Kennany, a member of the Egyptian Social Democratic Party, said he was detained and beaten last month on charges of insulting an army council member during a demonstration near the house of a general in Cairo.
"We were just standing silently holding up posters about the constitution," said Kennany, 26. "On my way home some plainclothes men tied my arms, blindfolded me and threw me to the ground. They just kept beating us, unthinkingly.
"We found ourselves on a floor of a civilian jail that housed dangerous criminals. The truth is we found among those criminals more humanity than the officers and informants.
"We were lucky that our party backed us and helped us, but there are thousands inside those jails that nobody knows anything about," said Kennany.
On August 12, Mursi pensioned off Field Marshal Hussein Tantawi, Mubarak's defense minister for 20 years, replaced the chief of staff and cancelled constitutional provisions that conferred wide powers on the army leadership.
The move gave Mursi powers rivaling those of Mubarak. It also removed any doubt that he would be able to release or retry the detainees facing military trial.
"It gives us new grounds to push for all our demands," said Abdel-Gelil of No to Military Trials. "Now he has the legislative and executive power to take the actions he should have taken from the start."
Campaigners say a new constitution being prepared must bar military courts from trying civilians - a practice employed under Mubarak to muzzle Islamists and other political opponents.
At the moment, an army decree still allows troops to arrest civilians on drug charges or on the vague crime of "thuggery".
Mohamed El Zarea, a rights lawyer and member of the committee Mursi appointed to review the military trial cases, said the body would recommend a civil retrial of all the civilian cases it is handling when it issues its final report, due by the end of August.
Critics of the process say the committee risks overlooking the many others detained by the army in often chaotic and arbitrary round-ups.
Others say Mursi seems to be looking after his political allies first; last month he pardoned at least 17 Islamists jailed for militancy during the Mubarak era.
"Mursi is biased because the youth in those jails are not part of his political current," said Samir Ghattas, head of the Middle East Forum, a Cairo-based think tank dealing with regional issues.
(Additional reporting by Tom Pfeiffer; Editing by Sonya Hepinstall)