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Under the deal, Muslim rebels agreed to disband guerrilla forces, surrender weapons and rebuild their communities while the government gives them self-rule with wider powers.
The Philippines and its largest Muslim rebel group, the Moro Islamic Liberation Front (MILF), on Thursday signed a final peace pact, ending about 45 years of conflict that has killed more than 120,000 people in the country's south.
The fight against Muslim separatists and Maoist guerrillas for almost five decades has stunted growth in resource-rich rural areas, besides scaring off potential investment in mines, plantations, energy and infrastructure.
Under the pact, Muslim rebels agreed to disband guerrilla forces, surrender weapons, and rebuild their communities while the government gives them self-rule with wider powers to control their economy and culture.
But potential threats to lasting peace remain, ranging from a small breakaway MILF faction to criminal gangs, Islamist militants linked to Al Qaeda and feuding clans, all a reminder to potential investors that region is volatile.
President Benigno Aquino and Malaysian Prime Minister Najib Razak, who briefly put aside his own country's problems over a missing Malaysia Airlines jet to witness the event, smiled and clapped as peace panel leaders signed the autonomy deal.
"Let us exchange our bullets for ripening fruit, our cynicism for hope, our histories of sorrow for a future of harmony, peace, and prosperity," Aquino told a gathering of officials, diplomats, lawmakers and Muslim community members.
"I will not let peace be snatched from my people again."
The event marked the final chapter in stop-start negotiations that lasted 17 years.
Malaysia, which has facilitated the peace talks since 2001, pledged its continued support.
"Much work remains, and there will be setbacks along the way," Najib said. "But the commitment to peace — the commitment I see in this room today — must not waver.
The final peace deal incorporates all agreements by the two sides, including annexes on power and wealth-sharing, and the creation of a police force for the autonomous Muslim area.
"The comprehensive agreement on the Bangsamoro is the crowning glory of our struggle," Muslim rebel leader Al Haj Ebrahim Murad said, in a reference to the new region, which takes for itself the name used for Muslim and non-Christian natives of southern Mindanao island.
He invited other Islamic groups, such as the Moro National Liberation Front, which opposed the deal, to join the new Bangsamoro political entity.
The next important step is the drafting and passage of the Bangsamoro Basic Law, which Aquino said would be a priority step. Both houses of Congress promised to pass the bill this year to create a new entity and expand the existing Autonomous Region in Muslim Mindanao.
A plebiscite later in Muslim-dominated areas in the south will determine the shape and size of the new region.
The government aims to put in place by 2015 the Bangsamoro Transition Authority, serving as an interim government, Aquino said, before elections in 2016, when his term ends.
Thousands of MILF fighters and supporters gathered under colorful tents at the Muslim rebel camp in Maguindanao to celebrate the conclusion of the deal. Elsewhere in Mindanao, thousands of Muslims held prayer rallies and celebrations.
"The mood is very festive," said MILF official Nasrullah Abdullah. "We are so overwhelmed that members and supporters flocked here to the camp."
Here are the key points of the deal, via Agence France-Presse:
TITLE: Called the "Comprehensive Agreement on the Bangsamoro." The Bangsamoro refers to people who at the time of Spanish conquest and colonization were considered natives or original inhabitants of the southern Philippines. Their descendants and spouses are recognized as Bangsamoro people.
Bangsa is a local word for nation. Moro derives from the term "Moors" used by Spanish colonialists to refer to Muslims.
AUTONOMY: The MILF drops its claims for a separate state in the southern region of Mindanao and settles for parliamentary self-rule in the Bangsamoro autonomous region. This will be established by 2016. The Bangsamoro will replace another Muslim autonomous region that was brokered in the 1990s with the MNLF, which the government says has failed.
DISARMAMENT: The MILF will "gradually" decommission its forces and put the weapons "beyond use." A local police force will assume law enforcement functions from the Philippine police and military.
POWERS: The Philippine government will retain exclusive powers on defense, foreign policy, currency and citizenship matters.
TAXES/REVENUES: The autonomous government will receive 75 percent of all local taxes, fees and charges, 75 percent of revenues from metallic minerals and control of fishing areas up to 12 nautical miles from the coastline.
ISLAMIC LAW: The region will not be an Islamic state, rather a secular government. Sharia law will apply only to Muslims and only for civil cases, not for criminal offenses. All residents are guaranteed basic rights to life, movement, privacy, and freedom of religion and speech.
TERRITORY: To cover five provinces, plus two cities, six towns and 39 villages in the south, comprising about 10 percent of the Philippines' total land area.
ENABLING LAW: Aquino is to ask parliament to pass a "Bangsamoro Basic Law" for the autonomous region by the end of this year.
PLEBISCITE: People living in areas to be included in the autonomous region will need to ratify the law in a plebiscite to be held in 2015.
TRANSITIONAL AUTHORITY: After the basic law is approved and ratified by the plebiscite, a 15-member "Bangsamoro Transition Authority" will govern the region until a regional parliament is elected. Aquino appoints the members of the transitional authority, but the MILF will have a majority and the chairman.
ELECTIONS: A regional parliament, expected to have 50 seats, is to be elected in conjunction with national elections in May 2016.