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Thousands of Syrians who had fled fighting began to return to their homes Friday after the Syrian rebels in southern Syria reached an agreement with Russia. Russia is a key ally of the Syrian regime and had been leading talks for a ceasefire.The rebels agreed to hand over heavy weapons and some of their areas of control near Dera’a.The deal is good news for the Syrian regime, Iran, Russia and Hezbollah, who have all won this round, easily vanquishing the rebels in the south after seven years of civil war. It is also good news for Jordan because it means that the massive pressure of around 200,000 civilians who had fled fighting toward Jordan’s border will now let up since they are likely to begin returning home.However, for Israel, the deal may not bring peace. The full details of the agreement are unclear but it does not appear to include the areas of Syrian rebel control adjacent to the Golan Heights. It also does not include the area of Islamic State control near the Golan. That means that Israel’s security interests are not part of the deal. In fact, Iran’s Press TV state media has celebrated the deal claiming it will now undermine Israel’s “collaboration” with the “militants” next to Quneitra and its control of the Golan.On Friday, Israel responded to an errant shell that fell on its side of the 1974 cease-fire line on the Golan Heights by striking a Syrian regime position on the other side.This does not bode well for the period ahead. There are a plethora of concerns for Jerusalem.First and foremost is the presence of Iran in Syria and Iranian-backed militias who took part in the recent offensive. Israel has said that Iran must leave Syria as the war winds down, but its militias are also active in the south. Furthermore, Hezbollah is active not far from Quneitra. As the rebels lose control, these anti-Israel forces continue their drive for control of the area near the Golan.Then there is the question of the thousands of Syrian civilians who have sheltered next to the Golan border.They have arrived over the last two weeks and Israel has supplied them with humanitarian aid. Many of these civilians fear the Syrian regime’s brutality and revenge attacks. Will they be able to return home under a subsequent deal? Israel has been isolated in negotiations about southern Syria. This is partly its own doing; it is not a party to the Syrian conflict and has not taken in large numbers of refugees like Jordan, Lebanon and Turkey have.However, Israel has stressed numerous times that the Iranian threat in Syria is a redline. Towards that end there have been numerous air strikes – some declared and others reported in foreign media – in recent years. These tensions have increased dramatically since last year.An Iranian drone penetrated Israeli airspace in February and on May 20 rockets were fired by Iranian forces in Syria at Israel.Yet, even as Iran has been probing Israel to estimate Jerusalem’s response, Syrian regime leader Bashar Assad has told interviewers that Iranian forces are not present in Syria. Moscow has said that “foreign” forces should leave Syria. All this points to a multi-layered attempt by Iran to hide there, pretending its “official” forces are not present, while its tentacles of influence spread.For instance, in mid-June an Iranian-backed Iraqi militia named Kata’ib Hezbollah found itself targeted by a mysterious air strike on the Syrian border with Iraq. This militia had set up a base on a strategic land corridor between Iraq and Syria. Damascus blamed the US for the strike, while the US blamed Israel.In some ways the defeat of the rebels in southern Syria marks the end of the Syrian conflict. The civil war began with protests in Dera’a. The rebels are either defeated, or have ended up under Turkish protection in the north.But a new round is beginning: the fight over the post-conflict era of Syria. That is a complex struggle involving the US and Turkey, but it also involves Israel.And for Jerusalem the main questions are whether Damascus will come out stronger or Iran will come out more of the winner in southern Syria, and what the Russian role will be. If the rebel deal near Dera’a succeeds, the regime will set its sights on the Golan border area and all of these questions will take on greater importance.