The war in Ambon and the wider Maluku islands started for a variety of reasons. But it quickly boiled down to a question of identity, of Christians versus Muslims, as more than 5,000 people were killed and 500,000 were displaced from their homes between 1999 and 2002.

The religious passions and communal hatred stirred up in the war put a question mark over Indonesia's moves to build a democracy after 40 years of dictatorship. Could Indonesia's Muslim majority coexist with Christians and other religious minorities without an authoritarian hand on the tiller?

Sitting in Ambon's Joas Coffee House 13 years after the fighting ended, the answer is clear: Yes. And sitting across from me is Jacky Manuputty, one member of a brave group of local community leaders, Muslim and Christian alike, who have helped heal the wounds of war and today act as the first responders of harmony when the fragile peace looks threatened.

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Filed under: * Culture-Watch • Religion & Culture • Violence • * Economics, Politics • Defense, National Security, Military • * International News & Commentary • Asia • Indonesia • * Religion News & Commentary • Inter-Faith Relations • Other Faiths • Islam • Muslim-Christian relations

When protests against the low-budget, anti-Islam "Innocence of Muslims" video flared across the Islamic world last month, Indonesia's Habib Munzir Almusawa preached a different message to his tens of thousands of followers in Jakarta: Just ignore it.

"If we react so emotionally, then how can we show the good side of Islam?" Mr. Almusawa told worshipers at the al-Munawwar mosque here....

Indonesia, the world's largest Muslim-majority nation, is seeing a wave of new, more moderate Muslim preachers, among them Mr. Almusawa. They represent a balancing of the more militant strains of Islam that have proliferated here. Ten years ago this week, Muslim extremists bombed nightclubs on the resort island of Bali, killing 202 people in the single biggest terror attack since Sept. 11, 2001, in the U.S.

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A West Java church which has become emblematic of record-breaking religious intolerance in Indonesia will now be relocated by the Indonesian government.

Taman Yasmin Indonesian Christian Church (GKI Yasmin) legally acquired permission to build a church in Bogor in 2006 but has been shuttered for years due to opposition from neighboring Muslim extremists. The Constitutional Court, the archipelago's equivalent of the U.S. Supreme Court, ruled in 2011 that the church be allowed to occupy its building. The mayor of Bogor refused to comply.

The government's recent decision came after a closed-door meeting between the Indonesian Minister of Internal Affairs and Bogor city leaders excluded GKI Yasmin church representatives but did include representatives from a local Muslim extremist group. According to ministry spokesman Reydonnyzar Moenek, the government is preparing replacement land for the church.

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Every few months, the head of counterterrorism in the world’s most populous Muslim nation pays a visit to a Koranic academy south of the capital to address an assembly of clerics. His message, he says, is blunt: Stopping would-be bombers “is your job, not mine.”

Ansyaad Mbai’s plea for help is also surprising, given the string of successes against Islamist militants that Indonesian security services have notched in recent years. After a blaze of attacks inspired in part by al-Qaeda’s Sept. 11, 2001, strikes in the United States, the militants in Indonesia are now a battered and diminished force. In just over two years, 33 terrorism suspects have been killed, mostly in shootouts with police, and nearly 200 have been arrested.

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It is fashionable these days for Western leaders to praise Indonesia as a model Muslim democracy. Secretary of State Hillary Rodham Clinton has declared, “If you want to know whether Islam, democracy, modernity and women’s rights can coexist, go to Indonesia.” And last month Britain’s prime minister, David Cameron, lauded Indonesia for showing that “religion and democracy need not be in conflict.”

Tell that to Asia Lumbantoruan, a Christian elder whose congregation outside Jakarta has recently had two of its partially built churches burned down by Islamist militants. He was stabbed by these extremists while defending a third site from attack in September 2010.

This week in Geneva, the United Nations is reviewing Indonesia’s human rights record. It should call on President Susilo Bambang Yudhoyono to crack down on extremists and protect minorities. While Indonesia has made great strides in consolidating a stable, democratic government after five decades of authoritarian rule, the country is by no means a bastion of tolerance.

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Violence against Christians in Indonesia frequently makes news headlines. However, acts of violence targeting Christians should not obscure the fact that the majority of Indonesia’s Christian communities live and worship free from fear and interference in a Muslim majority country, and that religious conversion has never been prohibited.

In the past few years, however, the level of religious freedom has declined. The government must have the courage to stop this trend and protect Indonesia’s religious minorities to continue to uphold religious freedom.

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The world’s most populous Muslim-majority nation, Indonesia, has long had a problem in some parts of the archipelago with religious extremism, intolerance and the sort of terrorism that can flow from both. The country has had a good deal of success in combating Islamist terrorism since the bombings on the island of Bali in 2002, which killed 202 people. But continuing suicide-bomb attacks and the discovery of terrorist training-camps suggest that Indonesia remains in danger. Judging by recent events, however, the country has yet to develop a clear strategy to deal with the threat. Too often, different bits of the state give out different, even contradictory, signals. The result is a dangerous muddle.

Thus on October 12th lawmakers at last passed a new security bill, the Law on State Intelligence. This was the culmination of years of debate, in many ways a tribute to Indonesia’s vibrant new democracy. Legislators wanted to produce a bill that sharpened the effectiveness of the country’s multitude of intelligence and anti-terrorist agencies without encroaching too much on hard-won civil rights. In the end, the law redefined the roles of those agencies, strengthening their powers to intervene against “opponents” working against the “national interest”. A tough new stance from the state, it might seem. Indeed, just the sort of law that might have made it easier to gather evidence against people such as Abu Bakar Basyir, a notorious radical cleric. At the conclusion of the latest case against him in June, Mr Basyir was sentenced to 15 years in prison by a district court for inciting terrorism and funding terrorist cells.

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When Dani bin Misra was released from prison last week after serving just three months for smashing in the skull of a member of a Muslim sect, this conservative Indonesian town let out a triumphant cry.

"He's a hero!" Rasna bin Wildan said of the teenage killer.

The ferociousness of the attack, captured on video and circulated widely on the Internet, guaranteed no one from the Ahmadiyah group would dare set foot in Cikeusik again, the 38-year-old farmer said as others nodded in agreement.

Their reaction is part of a wider wave of intolerance against religious minorities that is challenging Indonesia's image as a beacon of how Islam and liberalism can coexist.

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Days after rumors spread across this industrial city that Christians were conducting a mass baptism, hard-line Islamic leaders called for local mosques to create a youth guard to act as moral police and put a quick stop to forced conversions.

They started training early Saturday morning, around 100 young men turning out in a field in Bekasi wearing martial arts uniforms. Leaders stressed that there was no plan to arm them, but they do not shy away from saying they'll act essentially as thugs.

"We're doing this because we want to strike fear in the hearts of Christians who behave in such a way," said Murhali Barda, who heads the local chapter of the Islamic Defenders Front, which pushes for the implementation of Islamic-based laws in Bekasi and other parts of the archipelagic nation. "If they refuse to stop what they're doing, we're ready to fight."

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Indonesia's leading clerics are considering a religious edict against riding a motorbike without a crash helmet to promote safety on the chaotic and deadly roads of the world's most populous Muslim country.

Such a fatwa would not carry a penalty for those who ignore it, but advocates said Sunday making road safety a moral issue could be more effective than the law.

Helmets have been compulsory in Indonesia since 1988, but a 2005 government study found that up to 30 percent of riders in cities still did not wear one. Even fewer riders wear them in rural areas.

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In the months ahead, as 30,000 additional heavily armed American soldiers and Marines surge into Afghanistan, a much smaller group of young Americans will ship out to the world's most populous Muslim country: Indonesia.

Armed with little more than laptops and textbooks, shod not in combat boots but in sandals and sneakers, these 25 volunteers will be the first representatives of the Peace Corps to land in Indonesia since the organization was expelled in 1965. By agreeing to dispatch volunteers to live side-by-side with Indonesians, teaching English to their children and exchanging insights into each other's cultures, the Obama administration is sending the clearest possible signal to the world's Muslims: America's fight is not with you, but with the terrorists at your fringes.

The move also reflects recognition by the administration and Congress that the Peace Corps is a critical component of a new "smart power" policy toward U.S. engagement abroad. Such an approach emphasizes public diplomacy and grassroots-level development assistance over military hard power. Acknowledging the need for this shift, Congress voted last month to raise Peace Corps funding by $60 million — the largest increase ever — to $400 million.

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Indonesia has received a lot of bad press in recent years: for bombings in Bali and at the J.W. Marriott Hotel in the capital, Jakarta — both the work of al-Qaida-linked militants — and for numerous attacks on Christian churches. But Indonesia overall is a far more tolerant place than these acts suggest, and it appears to be getting even more accepting.

Indonesia is home to more Muslims than any other nation. But in Jakarta, a $27 million Christian church that seats more than 4,500 people opened its doors last month. The Reformed Millennium Cathedral is the work of preacher Stephen Tong, a sprightly 67-year-old who waited 16 years to get permission to build his church.

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