Season 7 Finale Spoiler Summery

• The last 3 years have all been a lie - Time has been rewritten. 
• In a timeline we haven't been shown directly but this one has been created to overwrite, in order to prevent something from stealing the Tardis the Doctor was forced to blow the ship up, killing his long term companion Clara Oswald in the process and trapping himself inside a time-loop forever watching her die. Not to be cheated of its prize the villain uses the moments left to it to use the Tardis to re-write time, rewriting the Timelords History in the process so as - in this reality (the one we've seen) the villain wins and the Doctor will never have been able to destroyed the Tardis.
• The Silence are not an alien species - they're biological off-shoots of the Tardis own Architectural Reconfiguration system - it's why they are memory proof. They're literally built out of Tardis.
• River Song cheated her death in the Library a bit like the Doctor cheated his death at lake Silencio.Though the Library version of River was wholly flesh and blood, she was literally the equivalent of a River Song wearing a River Song suit. The real River was stored in the Data-stick
• Clara is the Doctors original companion from the other timeline. In that reality he never crash-landed in Leadworth shortly after regenerating, never travelled with Amy Pond. Clara has always been his companion since his 11th incarnation began.
• The reason there are so many Clara's is that the original Clara was trapped in the Tardis Library when the Doctor blew up the ship - the Tardis was trying to save her but had nowhere onboard to send her so it tried to send her somewhere safe off-ship, most probably where-ever the Doctor is. Unfortunately, an exploding Tardis exists at all points in time and space simultaneously.
• The message Run You Cleaver Boy and Remember was implanted into Clara's data-pattern saved by the Tardis by the digital version of River uploaded into CAL.
•  The Doctors past has been radically re-written from the original - the consequences of that carry over to the Anniversary Special.
• Pretty much everything you think you know is a lie.

I hope that helps. Probably won't leading up to the finale, but when look back you'll see where it all occurred.

More to follow concerning the Anniversary, soon.

RED.