Decades of military brutality have left two provinces, Aceh and Irian Jaya, clamouring for independence.
Local independence wars are also being waged in Aceh, in north Sumatra, and in Irian Jaya.
IR You dismiss Irian Jaya as merely one of a number of independence wars currently being waged.
As in the Congo, the people of Irian Jaya have no political influence outside their country.
But the agreement so far only involves one of several OPM groups fighting against Indonesian rule in Irian Jaya.
The winners will also have to deal with other separatists' demands in provinces such as Aceh and Irian Jaya.
At the time, the military leadership warned that it would not tolerate open displays of anti-Indonesian feeling in Irian Jaya.
There has been a marked increase in separatist activity in Irian Jaya since the change in government in Jakarta in May.
Freeport McMoRan will get only 3 tonnes of copper from a 360-tonne truckload at its Irian Jaya copper mine in Indonesia.
The army is not, but it is hated in many places, especially in the separatist-minded provinces of Aceh and Irian Jaya.
Elsewhere, notably in Aceh at one tip of the straggling archipelago, and in Irian Jaya at the other, secessionist sentiment remains strong.
Certainly things don't look good in West Papua (formerly known as Irian Jaya, and home to extensive deposits of gold and other minerals).
Separatist sentiments are strong in Aceh, where six more people were shot dead last week, as well as in East Timor and Irian Jaya.
The army's domestic critics are not just concerned about its thuggery in East Timor, but also in other separatist provinces, such as Irian Jaya.
Serious trouble has already scarred the provinces of Maluku and Aceh, and more could be brewing in Sulawesi and Papua (formerly known as Irian Jaya).
After East Timor won its freedom last year, the desire for independence grew in provinces such as Aceh and Irian Jaya (recently renamed West Papua).
With the eyes of the world on Irian Jaya, there's at least a reasonable prospect that Jakarta is in a mood to listen to grievances.
He might even re-explore the idea of a Melanesian federation including West Papua, Papua New Guinea and Bougainville, ethnically a much healthier destiny than Irian Jaya.
Most worrying of all, Miss Megawati is likely to take a harder line towards separatists in Aceh and Irian Jaya, making any lasting solution even harder to achieve.
This is aimed at cutting off what little international support there might be for separatist rebels in the Indonesian provinces of Aceh and West Papua (formerly Irian Jaya).
Irian Jaya is Indonesia's largest, richest and least integrated province.
They are banking on a big enough change at the centre that they can talk not only the East Timorese around, but also separatist groups in other provinces, such as Aceh and Irian Jaya.
Results from the "fraying edges" - the restive regions of Aceh, East Timor, Irian Jaya and Maluku - have been slow to come in as well, and official tallies from those areas are still unavailable.
The aim could be to use the fate of East Timor as a dreadful warning to separatists in other parts of Indonesia, such as Aceh and Irian Jaya, if they too tried to break away.
The conflict in West Kalimantan does not threaten the integrity of the state in the way that separatist movements do in East Timor (which will vote on autonomy proposals after the election), Irian Jaya and Aceh.
Unlike the separatist movements in mainly Christian East Timor and Irian Jaya, which evoke little sympathy among Indonesia's Muslim majority, the repression in Aceh is considered by Islamic groups to be one of their core grievances against the Suharto-era army.
Mr Habibie needs to start working out the details of such reforms quickly, if he is to hold back a tide of anger over past atrocities, not only in Aceh but in East Timor, Irian Jaya and elsewhere in this diverse nation of islands.
Separatist movements exist in Madura, Kalimantan and the Moluccas, though they are puny in comparison with the two best organised, in Aceh on the northern tip of Sumatra, and, at the other extremity, in West Papua (formerly called Irian Jaya, and before that West New Guinea) some 4, 000km (2, 500 miles) away to the east.
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