Following the judge's veredict of the Catalan politicians who coordinated the "proces", or series of political movements to attempt to secede Catalonia from Spain; demonstrations have arisen within Catalonia protesting said judgement - the politicians were essentially deemed as conspirators against the Spanish constitution and have been given varying prision sentences. Parts of those demonstrations have turned violent: clashes with police trying to stop blockages of streets and railroads, burning of cars and dumpsters, etc...
The Catalonian government's stance on this is difficult: as a pro-independence government they're trying to promote actions against the veredict but in some situations it has gotten out of hand and turned violent - something a government can't really condone.
Tsunami Democratic is an organisation that has been coordinating demonstrations and developed an app that allows people to know where demonstrations are happening, etc - whether these demonstrations turn violent or not is officially out of their control; the Spanish authorities (in this case, a judge in charge of investigating the circumstances around the more violent parts of the rioting) obviously believe that the app is aiding in coordinating violent attacks - whether that's terrorism or just violent rioting is something I don't know and I'm unsure we'll ever fully know.
That's the context, at the end of the day it's a national government asking for a repo to be taken down in accordance to the laws of their country, you might disagree with it happening fundamentally but its nothing new, the Github repo for takedowns has plenty - although they seem to usually be coming from China/Russia.