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ISLAMABAD — The prospect that Pakistan’s president, Gen. Pervez Musharraf — who seized power in a bloodless coup five years ago — will remain head of the military looms as a major setback in the political outlook for South Asia’s second-largest nuclear-armed country.

Although Pakistan has been under military rule for more than half of its 57-year history as an independent nation, Musharraf’s status as president and military chief provokes fresh concerns in a number of areas.

A year ago Musharraf’s promise to step down as head of the military by yearend was viewed as crucial to weaning Pakistan’s powerful defense forces off politics. If Musharraf had retired, he would have still served as president till 2007, retaining most of his powers including that to sack an elected Parliament.

His broken promise is a powerful reminder of the ways in which Pakistan’s previous military rulers have demonstrated their penchant for staying in office indefinitely. The one before Musharraf, Gen. Mohammad Zia ul-Haq, seized power in 1977 with a promise to return to the barracks within 90 days, but ended up ruling the military and the country for almost 11 years.

Musharraf’s decision may well be hailed in foreign capitals such as Washington, where he is acknowledged as the principal ally in the so-called war on terror, but the course he has set for himself is bound to aggravate domestic problems, including those linked to the nation’s role as a major host for militant groups even before the Sept. 11, 2001, New York terrorist attacks.

Pakistan’s political system is bound to erode further as it increasingly comes under the dominance of a single military ruler. In this environment, Parliament’s role as a credible decision-making body on long-term policy issues related to fighting terrorism will likely weaken.

Additional fallout includes the danger that Pakistanis may consider the existing representative forum inadequate and begin resorting to their own solutions to community problems rather than wait for the politicians. Such an outcome would differ little from that in other countries where failed political systems have led to anarchy and chaos.

Of equal significance is the future of the Pakistani economy and its relationship to the country’s overall outlook. The New York terrorist attacks prompted Pakistan to become a close U.S. ally. The reward for Pakistan’s services in support of the U.S. military campaign in Afghanistan was economic assistance — new funds as well as help in restructuring part of Pakistan’s foreign debt.

Despite this largess, almost one-third of Pakistan’s population of 150 million lives below the poverty line. Such a large community of impoverished provides a fertile resource for militant groups. Thus the ability of any government to use its economic success for the eventual benefit of its population cannot be separated from its political system.

Pakistan is long overdue for reform of its system of social services, the networks responsible for internal security and the institutions that are supposed to ensure the fundamental rights of citizens. The erosion of representative politics — the likely outcome of Musharraf’s remaining in power — will further set back prospects for such reform.

While Musharraf may well disregard the argument that his increasingly unassailable position will aggravate Pakistan’s political and economic challenges, he must not ignore a vital lesson of recent history: Leaders and countries without clear-cut succession plans are likely to experience periods of uncertainty.

Ultimately, progress in Pakistan will mean making a transition to true representative politics — ending the all too familiar legacy of interruptions every few years followed by new beginnings.

If Musharraf were able to change his view to the extent that he established a new tradition by overseeing a smooth transition to civilian and representative rule, he would be lauded in Pakistan for generations to come as a political pioneer. But if history is any indication, this is unlikely to happen.

Previous Pakistani rulers have time and again demonstrated their zeal to stay in charge, irrespective of the compelling case against that choice.

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