Egypt's constituent assembly worked through the night to finish voting on Egypt's new constitution, finalizing its work early this morning and sent the contentious document to the president, who will call a national referendum on the constitution within two weeks.

President Mohamed Morsi's allies made the surprise move to finish the document this week after he issued a decree sidelining the judiciary and removing nearly all checks on his power.

Though the constitution's content had been the subject of debate for months, the process of drafting it was more controversial than the text itself. The first body elected to write it was dissolved by a court after secularist members complained it was dominated by Islamists. The second body, elected by a now-dissolved Parliament, was likewise packed with Islamists and negotiations over revising its makeup broke down months ago, with some secular parties announcing they would boycott the assembly.

Most of the remaining non-Islamist members, including all Christian members, left the committee over recent weeks, complaining their suggestions were ignored.

The rush to complete the document this week – the president's decree had extended the deadline for its completion by two months – infuriated the opposition, who say a flawed, unrepresentative document is the result. Thousands of people protested the new draft constitution in Tahrir square today.

Zaid Al Ali, a Cairo-based adviser on constitution building for the Institute for Democracy and Electoral Assistance, says: "A major opportunity was missed to really study what went wrong under the previous system" and try to address those problems. While focusing on disagreements between Islamists and secularists, the drafters missed an opportunity to address issues like decentralization of power, effectiveness of governance, and corruption.

Others had hoped the constitution would do more to achieve social justice and alter what they say is a state structure that contributes to the growing gap between rich and poor.

But many expect the constitution will pass a national referendum, because of the Muslim Brotherhood's ability to mobilize its grassroots and because many Egyptians are eager to see the instability of the past 22 months come to an end, and believe a permanent constitution will help achieve that.

While the process was contentious, here is a look at the actual content of the new constitution on key issues:

Islam and the state

Islamists and non-Islamists engaged in extensive wrangling during recent months over the role of Islam in the state, and the specific wording that would be used in the constitution to define how sharia, or Islamic law, relates to legislation. In the end, the drafters preserved the wording of the previous constitution: The principles of sharia are the main source of legislation. However, they also added another clause specifying what is meant by the principles of sharia.

That clause says the principles of sharia should be in accordance with the established schools of Sunni Muslim doctrine. This limits the discretion given to judges in deciding on sharia issues, and could limit them from applying a progressive interpretation of sharia. But it could also keep judges from drawing on more extreme or conservative interpretations of sharia, say rights activists.

Also included in the constitution is an article stipulating that scholars of Al Azhar, the university and mosque considered one of the most respected centers of Sunni Muslim research and learning, be consulted on matters of sharia. It does not make the Al Azhar scholars' opinion binding.

It is the first time that a consultative role for Al Azhar has been enshrined in Egypt's constitution.

Both of these articles are dangerous, says Michael Hanna, a fellow at The Century Foundation who tracks Egyptian politics. "What that does is begins to shift all the terms of discourse away from the civil law system and toward religiously-based strictures," he says. "Al Azhar is enshrined in the text. Sunni jurisprudence is enshrined in the text. It begins to shift the terms of reference and privileges a certain discourse that is religiously based."

Rights and freedoms

The constitution contains one article that makes a broad provision for free expression. But Heba Morayef, Egypt director for Human Rights Watch, says the drafters failed to include crucial language explaining how that right may be limited, which is needed "to make sure that the limitations are narrow and there's no abuse," she says.

Instead, they included two additional clauses which limit free speech. One prohibits insulting prophets, and another prohibits insulting the "individual person." Both are vague enough that they can easily be used to limit freedom of expression and could lead to an avalanche of lawsuits. Blasphemy charges have jumped in the last year and a half, and charges of insulting the president and the judiciary have already increased since Mr. Morsi took office.

Freedom of religion has also been curtailed in the new constitution. Egypt's previous constitution guaranteed the freedom of religion and religious practice. The same wording was used in earlier drafts of the new constitution. But the document that was voted on last night only promises freedom of practice for the Abrahamic religions – Islam, Christianity, and Judaism.

This leaves other religious sects in Egypt, such as Egyptian Bahai'is, stripped of the right to publicly practice their faith.

"To say that they can't even practice their religious rights is terrifying," says Ms. Morayef. She notes that the limitation could easily be appled to Baha'is, who have already fought an uphill battle in Egypt just for the right to leave the religion section of their national identity cards blank. (ID cards include citizens' religion and the options are limited to Islam, Christianity, or Judaism.)

Under former President Hosni Mubarak, Baha'is, as well as Ahmadis, Shiites, and Quranists were regularly arrested for their beliefs.

Women

On women's rights, an article in a previous draft said women's equality was guaranteed so long as it did not contradict Islamic law. That clause was dropped completely from the final version.

But the article prohibiting discrimination fails to mention sex, or any other grounds, simply stating that "citizens are equal before the law and equal in rights and obligations without discrimination." While some rights activists feel the broader clause is better because it doesn't limit the prohibition on discrimination, Morayef says it could be detrimental for women's rights to not explicitly prohibit discrimination against them.

The only article that specifically mentions women's rights says that the state should "balance between a woman's obligations to family and public work" and provide "special protection" for single mothers, divorced women, and widows. The vague wording could give grounds for the state to interfere in a woman's rights – for example, if it decided a woman should not travel because she was not balancing her obligations to her family by doing so.

The same article states that the "state should commit to preserving the true nature of the Egyptian family," and the next article states that the state should "protect ethics and morals and public order."

According to Human Rights Watch, the language in these provisions is overly broad and could be used to restrict rights. What's more, the constitution says that the rights and freedoms it guarantees may be exercised as long as they do not contradict the principles in these articles. According to Human Rights Watch, that stipulation "appears appears to place the 'true nature of the family” and morals and public orders above fundamental rights."

But rights activists point to positive points in the new document, as well.

The document specifically mentions and prohibits torture, something rights activists had pushed for. Police abuse and torture, widespread under Mubarak and until now, was one of the main grievances of protesters during the uprising against the former president. The document also promises protection from arbitrary detention, another hallmark of the Mubarak years, and provides protection for freedom of movement, privacy of communication, and freedom of assembly and association, according to Human Rights Watch.

The military

The new constitution guarantees the Egyptian military many of the prerogatives it had sought to maintain since the transition began. The military's attempt a year ago to maintain its power and privileges brought thousands of protesters – including the Muslim Brotherhood – into the streets of Cairo.

Now, the constituent assembly dominated by the Brotherhood's Freedom and Justice Party has granted the military much, though not all, of what it wanted. The military's budget is protected from parliamentary oversight, one of its demands last year. The constitution provides for the establishment of a National Defense Council, whose members include government and military officials, that will oversee the defense budget and should be consulted on laws relating to the military. The constitution also mandates that the post of defense minister be filled by a military officer.

The constitution allows the continuation of military trials for civilians. After the military junta took control of Egypt when Mubarak stepped down, it sent more than 12,000 civilians before military tribunals, where the trials sometimes lasted for just five minutes and which rights groups say are inherently unfair. While a previous draft of the new constitution had stated that the military could not send civilians before military trials, the constituent assembly deleted that clause at the request of the military. The draft voted on yesterday states that civilians may be tried before military courts for crimes that harm the military "as defined by law." The military interprets that clause very widely under the military code of justice.

Balance of power

After the uprising against an authoritarian president, many in Egypt had argued the new constitution should shift the balance of power toward Parliament, reducing the power of the presidency. While the new constitution does not make Egypt a parliamentary system, it does give the Parliament more authority.

The new constitution limits the president to two four-year terms. It also requires parliamentary approval when the president's prime minister forms a new government. If the Parliament votes against the government twice, it is given the authority to form a government on its own.

"It's a complicated relationship. It's not the case that the president is elected, he appoints a prime minister who chooses a cabinet, and if the Parliament isn't happy about it it's their problem," says Mr. Ali, of the Institute for Democracy and Electoral Assistance. Parliamentary checks on presidential powers are now "very present," he says.

The Parliament's oversight over government is also increased in the new constitution. It is given new powers for forming special investigatory committees, says Ali, while it keeps the power to force government ministers or officials to appear before parliament for questioning.

One of the "worst" parts of the new text, according to Ali, is its continuation of the centralization of government in Egypt. The document keeps most authority with central government and does not empower local governments, or make them more accountable to the people.

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The new document delegates defining the power, mandate, and appointment of governors to legislation.

Under current legislation, governors are appointed by the central government, rather than elected. Elected governors was one demand of many of the protesters during the revolution. The constitution provides for the election of local councils, but strips them of any real power, stipulating that the central government will "answer requests for assistance" from local councils. "What that means is that the central government will be providing all essential services," says Ali. "What you're doing is you're electing people who don't have any authority. It's actually worse than not electing them at all."