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The power-sharing deal between the SNP and Scottish Greens is a "leap of faith" for both parties, Nicola Sturgeon has told MSPs.
The first minister was speaking as Holyrood approved the appointment of Green politicians to ministerial office for the first time anywhere in the UK.
She said the pact could represent "a new and better way of doing politics".
Holyrood's other parties hit out at the deal, saying it was more about pursuing independence than the environment.
However the SNP-Green majority in parliament was able to vote through the appointment of Patrick Harvie and Lorna Slater as junior ministers in the Scottish government.
Meanwhile, it has been confirmed that the Greens will no longer have a leaders question at First Minister's Questions or an automatic speaking slot at the start and end of Holyrood debates.
The cooperation agreement between the SNP and Scottish Greens was hammered out during the parliament's summer recess.
It technically falls short of a full coalition arrangement, with a range of areas set aside where the parties will be allowed to disagree over the coming years.
However it does see Green MSPs enter government, with co-leaders Mr Harvie and Ms Slater taking up posts focused on zero-carbon homes and green jobs.
Ms Sturgeon told MSPs that the deal was "a milestone in this parliament's progress", and a "commitment to a new and better way of doing politics".
She said it was "the product of much negotiation and some compromise, and also a leap of faith for both parties" - but "one we are taking willingly and for the common good".
The first minister said the deal would "provide the strong platform needed to deliver the transformative policies that will build a greener, fairer country and make people's lives better".
And she said delivering an independence referendum inside the current parliamentary term would be a "key strand" of the pact, saying there was an "undeniable" mandate for this.
One consequence of the deal has been that the Greens will have fewer opportunities to ask questions and table debates at Holyrood.
They will no longer have a regular place in the weekly session of First Minister's Questions or the right to respond to ministerial statements, and will have their allocation of "short money" funds cut.
However the remaining five Green MSPs on the back benches will still be able to table questions - with Mark Ruskell demonstrating this after Ms Sturgeon's statement by intervening to praise the deal.
Opposition parties were critical of the power-sharing arrangement, with Scottish Conservative leader Douglas Ross calling it a "nationalist coalition with one overriding goal - separating Scotland from the UK".
He said the SNP had needed to do the deal as they "failed to get a majority" in May's election, and said it would "hammer everyone who works hard, everyone who runs a business and everyone who owns a vehicle".
Scottish Labour's Anas Sarwar said the move was "more about the constitution than the climate".
He said the pact was "not about delivering accountability and transparency", but about "greater control for Nicola Sturgeon and the SNP".
And Lib Dem leader Alex Cole-Hamilton said the agreement was "thin gruel for the Green Party", claiming the "SNP have barely had to budge" on key policies such as education.