The New York Times has published a long analysis of the effects of the hacking of Democratic Party organisations and operatives in the 2016 election campaign.
The article is obviously trying to appear a balanced view, eschewing the "OMG we are at war with Russia" hyperbole and questioning the value of different pieces of evidence. It does slip here and there, for instance jumping from the involvement of "a team linked to the Russian government" (for which there is considerable evidence) to "directed from the Kremlin" without justification.
The evidence that the hackers who penetrated the DNC systems and John Podesta's email account are linked to the Russian Government is that the same tools were used as have been used in other pro-Russian actions in the past.
*Update 4th Jan 2017: that is a bit vague: infosec regular @pwnallthethings goes into very clear detail in a twitter thread)
One important consideration is the sort of people who do this kind of thing. Being able to hack systems requires some talent, but not any weird Hollywood-esque genius. It also takes a lot of experience, which goes out of date quite quickly. Mostly, the people who have the talent and experience are the people who have done it for fun.
Those people are difficult to recruit into military or intelligence organisations. They tend not to get on well with concepts such as wearing uniforms, turning up on time, or passing drug tests.
It is possible in theory to bypass the enthusiasts and have more professional people learn the techniques. One problem is that becoming skilled requires practice, and that generally means practice on innocent victims. More significantly, the first step in any action is to work through cut-out computers to avoid being traced, and those cut-outs are also hacked computers belonging to random victims. That's the way casual hackers, spammers and other computer criminals work, and espionage hackers have to use the same techniques. They have to be doing it all the time, to keep a base of operations, and to keep their techniques up to date.
For all these reasons, it makes much more sense for state agencies to stay arms-length from the actual hackers. The agencies will know about the hackers, maybe fund them indirectly, cover for them, and make suggestions, but there won't be any official chain of command.
So the hackers who got the data from the DNC were probably somewhat associated with the Russian Government (though a comprehensive multi-year deception by another organisation deliberately appearing to be Russian is not completely out of the question).
They may have had explicit (albeit off-the-record) instructions, but that's not necessary. As the New York Times itself observed, Russia has generally been very alarmed by Hillary Clinton for years. The group would have known to oppose her candidacy without being told.
"It was conventional wisdom... that Mrs. Clinton considered her husband’s efforts to reform Russia in the 1990s an unfinished project, and that she would seek to finish it by encouraging grass-roots efforts that would culminate with regime change."
Dealing with the product is another matter. It might well have gone to a Russian intelligence agency, either under an agreement with the hackers or ad-hoc from a "concerned citizen": you would assume they would want to see anything and everything of this kind that they could get. While hacking is best treated as deniable criminal activity, it would be much more valuable to agencies to have close control over the timing and content of releases of data.
So I actually agree with the legacy media that the extraction and publication of Democratic emails was probably a Russian intelligence operation. There is a significant possibility it was not, but was done by some Russians independent of government, and a remote possibility it was someone completely unrelated who has a practice of deliberately leaving false clues implicating Russia.
I've often said that the real power of the media is not the events that they report but the context to the events that they imply. Governments spying on each other is completely normal. Governments spying on foreign political movements is completely normal. Governments attempting to influence foreign elections by leaking intelligence is completely normal. Points to Nydwracu for finding this by William Safire:
"The shrewd Khrushchev came away from his personal duel of words with Nixon persuaded that the advocate of capitalism was not just tough-minded but strong-willed; he later said that he did all he could to bring about Nixon’s defeat in his 1960 presidential campaign."
The major restraint on interference in foreign elections is generally the danger that if the candidate you back loses then you've substantially damaged your own relations with the winner. The really newsworthy aspect of all this is that the Russians had such a negative view of Clinton that they thought this wouldn't make things any worse. It's been reported that the Duma broke into applause when the election result was announced.
The other thing that isn't normal is a complete public dump of an organisation's emails. That's not normal because it's a new possibility, one that people generally haven't begun to get their heads around. I was immediately struck by the immense power of such an attack the first time I saw it, in early 2011. No organisation can survive it: this is an outstanding item that has to be solved. I wouldn't rule out a new recommended practice to destroy all email after a number of weeks, forcing conversation histories to be boiled down to more sterile and formal documents that are far less potentially damaging if leaked.
It is just about possible for an organisation to be able to adequately secure their corporate data, but that's both a technical problem and a management problem. However, the first impression you get is of the DNC is one of amateurism. That of course is not a surprise. As I've observed before, if you consider political parties to be an important part of the system of government, their lack of funding and resources is amazing, even if American politics is better-funded than British. That the DNC were told they had been hacked and didn't do anything about it is still shocking. Since 2011, this is something that any organisation sensitive to image should be living in fear of.
This is basically evidence-free speculation, but it seems possible that the Democratic side is deficient in actual organisation builders: the kind of person who will set up systems, make rules, and get a team of people to work together. A combination of fixation on principles rather than practical action, and on diversity and "representativeness" over extraordinary competence meant that the campaign didn't have the equivalent of a Jared Kushner to move in, set up an effective organisation and get it working.
Or possibly the problem is more one of history: the DNC is not a political campaign set up to achieve a task, but a permanent bureaucracy bogged down by inferior personnel and a history of institutional compromises. Organisations become inefficient naturally.
Possibly Trump in contrast benefited from his estrangement from the Republican party establishment, since it meant he did not have legacy organisations to leak his secrets and undermine his campaign's efficiency. He had a Manhattan Project, not an ITER.
The task of building--or rebuilding--an organisation is one that few people are suited to. Slotting into an existing structure is very much easier. Clinton's supporters particularly are liable to have the attitude that a job is something you are given, rather than something you make. Kushner and Brad Parscale seem to stand out as people who have the capability of making a path rather than following one. As an aside, Obama seems to have had such people also, but Clinton may have lacked them. Peter Thiel described Kushner as "the Chief Operating Officer" of Trump's campaign. Maybe the real estate business that Trump and Kushner are in, which consists more of separate from-scratch projects than most other businesses, orients them particularly to that style.