After six weeks in office Egypt's first civilian president has sidelined the military, forcing it to leave the political arena it controlled for six decades. What are the likely ramifications, asks Amira Howeidy When the ruling Supreme Council of the Armed Forces (SCAF) issued a constitutional addendum on 17 June -- the final day of the presidential election runoffs -- clipping the future president's wings while giving the military exceptional powers, it was clear that Egypt was in the throes of a power struggle. It was also clear that -- for the time being, at least -- the army had the upper hand. SCAF annulled parliament, claimed legislative powers, control of the budget and constituent assembly and formed a defence council dominated by generals to oversee military affairs. When the Brotherhood's uncharismatic Mohamed Mursi -- the group's back-up candidate for the presidential elections -- finally emerged the victor, he was forced to swear his oath of office before the Mubarak-appointed Supreme Constitutional Court. The president's weakness was underscored by the overweening presence of SCAF's head, 76-year-old Field Marshal Mohamed Hussein Tantawi. Mursi may have won the election but he was sharing the office of president. A hostile media campaign against Mursi only reinforced this impression. On Sunday 12 August the "puppet" president turned the tables, much more quickly than Mursi's most optimistic backers had dared to hope. Tantawi was forced into retirement, along with SCAF's deputy chief Sami Anan. After two decades as the military's strong man Tantawi was replaced by SCAF member Abdel-Fattah El-Sisi, the 57-year-old head of military intelligence. Eight SCAF members were moved in the reshuffle. Mursi also appointed a vice president. Mahmoud Mekki, 58, the former head of the Court of Cassation, was a leading figure in the 2005-2006 campaign for greater judicial independence that had proved such a thorn in the side of the Mubarak regime. To top it all, Mursi issued a constitutional addendum of his own which not only cancelled the military's 17 June supplementary declaration but allocated the powers SCAF had granted itself to the president. On Tuesday Mursi continued his reshuffle of the military by naming new commanders of air defence, naval and air forces. Mursi had pulled off a soft-coup. The legitimacy he has accrued by virtue of being elected democratically had proved stronger than many analysts thought. Strong enough, certainly, to allow Egypt's first non-military president to exercise his authority in a direction that is reshaping the bases of the Egyptian state. "One of the most significant elements of a modern democratic civilian state has been established," says military expert and former senior intelligence officer Safwat El-Zayat. "Do not underestimate the importance of the new minister of defence's salute before the civilian president who appointed him." Many SCAF members may remain on the scene, adds El-Zayat, but it's only a matter of time before public pressure corrects that. "We're still in a transitional phase. Radical changes won't happen overnight but the ball is rolling and it can't be stopped." While it is far from clear how the new constitution will define the relationship between the military and the state, El-Zayat predicts it will place military-civilian relations in a far "healthier" balance. Rabab El-Mahdi, one of a handful of Egyptian experts on military-civilian relations, offers a more cautious reading. The military may no longer be governing directly, she says, but their engagement in politics is far from over. "There's still a strong military presence in senior civilian positions and the military retains its economic power base. It still constitutes a major centre of power." Mursi's move came a week after gunmen killed 16 Egyptian border guards in Rafah. The attack initially appeared to damage Mursi. He was accused of allowing his ties with the Muslim Brotherhood, which is close to Hamas, to sway his judgement, downgrading security at the Rafah border crossing with Gaza and allowing Palestinian militants easy entry to Sinai. While no evidence has emerged to identify the assailants -- it was destroyed by the Israeli missiles that killed the attackers -- the mainstream media and SCAF were quick to claim Palestinian involvement. The tide against Mursi was so high it was deemed unsafe for him to attend the funeral of the border guards. When his prime minister, Hisham Qandil, turned up at the funeral prayers he was attacked by a shoe-throwing mob. Things began to change when general intelligence chief Mourad Mowafi revealed both the intelligence services and the army had been warned of the attack. Mursi responded by sacking Mowafi, the governor of North Sinai, the head of the Republican Guard and Hamdi Badin, the head of military police. The dismissals did little to contain growing unease over the military's failure to prevent the attack. Tantawi's subsequent decision to launch a major offensive in Sinai, involving the bombing of alleged terrorist strongholds, also failed to assuage the public outcry. It was against this backdrop that Mursi made his move against Tantawi and the military's elite. The "balance of power", says El-Mahdi, had tilted in Mursi's favour and he was "shrewd enough" to use it. The details of how Mursi orchestrated his coup are unlikely to emerge in the public domain. That there was no response from the military to the dismissals suggests Mursi acted with the support of senior officers. His promotion of El-Sisi to replace Tantawi was an astute move, since in his role as head of military intelligence he will know all the skeletons in the military's cupboard. Mursi clearly used disagreements within SCAF over the transitional period in his favour, and his powers of patronage -- awarding prestigious promotions -- appear to have been enough to secure the support of at least half of the military council's members. Important questions, though, remain unanswered. Were Mursi's moves as closely linked to the Rafah border attack as their timing suggests? A story published Wednesday in the Israeli daily Haaretz claims Mursi dismissed the generals to pre-empt a military coup planned for August. While the story conspicuously failed to provide any evidence for its assertions it feeds into the mystery surrounding the sackings. And how closely was the Muslim Brotherhood involved in Mursi's coup? If no one is holding their breath waiting for credible revelations of what actually went on between Mursi and Tantawi, they expect even less to emerge about the role of the Brotherhood. Commentators describe the Brotherhood's decision-making process, believed to be dominated by Khairat El-Shater, as the group's black box. It is shrouded in mystery. More than a year after it was formed the Brotherhood's Freedom and Justice Party's (FJP) links with the group remain vague. So too is the relationship between Mursi and both the Brotherhood and FJP. Mursi may have been able to use his legitimacy as elected president to dismiss the generals but such political capital comes with a sell-by-date. Without clearing up persistent questions about the influence of the Brotherhood over the presidency -- and that requires a commitment to transparency no one seems keen to embrace -- it may expire sooner than anyone supposes. Traces of Brotherhood influence can be found in Mursi's decision to name Mahmoud Mekki as his deputy, after appointing his brother, judge Ahmed Mekki, as minister of justice. The Brotherhood has long fetishised judges, approaching several in the hope one might agree to run as the group's presidential candidate. Ahmed Mekki is rumoured to have originally accepted the Brotherhood's offer only to change his mind. The Mekki brothers' appointments have been welcomed by many political forces on the strength of the leading role both played in pressing for greater judicial independence. On Tuesday Ahmed Mekki began moves to transfer the supervision of judges from his ministry to the Supreme Judicial Council, a huge step towards freeing the judiciary from executive control. Mursi emerged this week with his power consolidated. There is no longer a military to blame for any ensuing disaster. It is now up to the elected president to deal with Mubarak's ugly legacy. He will be judged on how far he succeeds.