The Syrian counter-terror agreement is ambitious, full of pitfalls and the best hope for a resumption of the ceasefire and peace talks in Syria.

The kernel of the agreement, reached after 13 hours of talks in Geneva on Friday, is a staged ceasefire, a reopening of humanitarian aid, followed by a grounding of the Syrian air force in those areas dominated by opposition fighters recognised by the west. A specific plan has been set out on how to deliver aid to the 250,000 citizens of Aleppo who are running out of water and fuel.

In return the west will coordinate with Russia not just attacks on the forces of Islamic State in north-west Syria, but also the al-Qaida-linked and recently rebranded Jabhat al-Nusra.

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For Russia’s foreign minister, Sergei Lavrov, the responsibility in the agreement lies in requiring the Syrian air force to ground itself over its sovereign territory, and in ensuring humanitarian aid – too often callously blocked by the Syrian army checkpoints – is allowed to flow again.

President Bashar al-Assad sees no distinction between the opposition forces, regarding them all as terrorists opposed to his regime. This agreement requires him to change that mindset.

For the United States, there is a responsibility to require the Washington-backed Syrian opposition to disentangle themselves militarily, politically and even physically from Jabhat al-Nusra.

In practice, there has been a marbling between al-Nusra and Washington-backed fighting forces as they unite against the military advance of Assad.

The Pentagon, and some in the state department, are doubtful that Russia has the means or the determination to control the Syrian air force. The new ceasefire is due to start 12 September, and they fear the US Secretary of State, John Kerry, has miscalculated.

The Washington-based Syria Institute said: “While Lavrov mentioned that they agreed on procedures on responding to any breaches or violations of the cessation of hostilities, no details were given. The lack of enforcement or compliance measures in previous agreements has been a key contributor to their failure.”

“Plans do not implement themselves,” Kerry pointed out. Details of how the agreement will be enforced, currently being kept private in five separate chapters, include the exchanges of intelligence, the maps delineating the precise distribution of opposition forces, and the sanctions for ceasefire breaches.

Lavrov insists he won the agreement of Assad in what they will see as the first east-west agreement to defeat not just Isis in Syria, but other jihadi groups. Russia has long sought US cooperation in this anti-terror battle.

Apart from the sincerity of Syrian cooperation, the second biggest question is whether western-backed Syrian fighters will disassociate themselves from al-Nusra.

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Kerry was unambiguous. “Going on al-Nusra is not a concession to anybody” but “is profoundly in the interests of the US,” he said

Bassma Kodmani, a senior figure in the main opposition body the High Negotiation Committee (HNC), insisted the marbling will end, and the cessation of hostilities will allow for the extremists’ influence to be marginalised. She said: “When the cessation of hostilities was installed in February, the opposition – 100 groups – respected it. It was violated by the regime. So a return to a cessation of hostilities has been our demand. We are absolutely in favour of it.”

Asked if opposition fighters will separate themselves from extremists, Kodmani said: “In the cessation in February, when our groups committed to it, the extremists were marginalised. They did not dare to challenge it. Since then opposition forces and extremists have been forced together under siege.

“So the key is ending Assad’s strategy of surrounding whole areas and besieging them. The moderate groups will reorganise and distance themselves from the radical groups. We will do our part.”

But Charles Lister, a senior fellow at the Middle East Institute and expert on the Syrian jihadis, was more dubious. He wrote: “Having spoken with leadership figures from several dozen armed factions in recent weeks, I can say that not a single one has suggested any willingness to withdraw from frontlines on which JFS is present. To them, doing so means effectively ceding territory to the regime, as they have little faith in a long-term cessation of hostilities holding.”

But he added: “The armed opposition in Syria now faces what is perhaps its biggest and most momentous decision since they chose to take up arms against the Assad regime in 2011. There is no hiding the fact that mainstream opposition forces are extensively “marbled” or “coupled” with JFS forces on frontlines from Deraa in the south, to Damascus and throughout the north-west of the country.”

One best option is that al-Nusra forces will withdraw knowing that to do otherwise would hinder the peace process, and lose fragile popular support. But the next few days will be a big test of the HNC influence on the ground.

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There is much that is absent from the agreement, including any commitments on the release of political detainees or any promise by either side to change their stance on the legitimate place for Assad in a future Syria. The previous peace talks designed to map out a transition to a new government did not really travel much past first base, mainly due to the Syrian opposition demand that Assad leave within six months.

The two sides did not even meet face to face, preferring to trade insults at sporadic press conferences, as the genteel UN special envoy Staffan de Mistura manfully looked for chinks of light amid the uniform darkness.

Since then, and only this week, the HNC set out a coherent road map to a new Syria that is recognisably democratic and does not assume anyone connected with the Assad regime will have to stand aside. It is a plausible alternative for the future of Syria, and one in which Russian influence is not eradicated.

But in the entrails of the Kerry Lavrov press conference, Lavrov highlighted the problems ahead in the peace talks, pointing out that the HNC cannot be seen as the sole negotiating body. He pointed to other groups – the Moscow and Cairo group – as requiring equal status in any peace talks. The HNC is seen as a creature of Saudi Arabia by the Russians, and representative mainly of Riyadh. So if talks do resume, the basics of the attendees may have to be revisited.

There are at least two further difficulties. The Kurds have a nominal role in the HNC, but its chief representatives are excluded. There was also no sign of Iran in these peace talks, yet they have militia fighting on the ground in Aleppo and elsewhere. Iran and Moscow interests do not fully elide in Syria.

So no one is pretending after so many setbacks that a corner has been turned, but at least it is possible to see if it can be reached.