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[FrancisJohn]

Is it possible to get all the colony enhancements in one run? (Soil Nanites, cryoengine, biofactory embro etc)
Is it possible to NOT get all the enhancements in one run?
Can you get some of the enhancements from quests, bar missions etc?
There are two know locations of pristine nano forges, is there any other known locations of things you can steal?
There is a mission "Flag down the academic with the Tri-Pad" in the bar, is this a repeatable mission does anyone know? If you don't send them the AI core does anything different happen?

[Megas]

Sindria and Natchiteka have Synchrotrons.  Eventide has a Spool.  Industry worlds that did not have Pristine Nanoforge have Corrupted Nanoforge instead.  Derelict Motherships can drop a forge as part of its loot.

Other colony items are randomly generated loot.

The historian can offer (randomly selected) colony items after the player knows most or all of the blueprints.  Cost is four story points for the first colony item, and doubles for each subsequent item.

There is a mission "Flag down the academic with the Tri-Pad" in the bar, is this a repeatable mission does anyone know? If you don't send them the AI core does anything different happen?

That mission is unique.  There is no downside for keeping the core.  The game notes your treachery in the intel, but there is nothing more in that quest line (yet).  The only other thing different is you do not trigger a possible pirate ambush (if you keep the core) that may be done if you send the core off to honor your bargain instead.  Basically, no good deed goes unpunished.

[Salter]

You can find some of those as random loot on core worlds you saturate bombard to death, but only if they have ruins.

Also if you get all the items or not is entirely by chance. I dont know if the game randomly generates loot when you interact with something or its all pregenerated like the systems are, but the smaller system you can start with at initial character creation means less chances for loot and so you might miss some of the items.

[Serenitis]

Is it possible to get all the colony enhancements in one run? (Soil Nanites, cryoengine, biofactory embro etc)

Yes.
Frequently multiples as well if you explore enough.
All planetary ruins can give these - the larger the greater chance.
Abandoned Mining stations frequently give them, Research stations sometimes, and Habitats never.
Derelict motherships will often give items, and survey ships can sometimes also drop them.
It is also possible (although v. uncommon) to find items within abandoned ships - although these must be the ships that are 'generated' by the procgen, not the drifting ships that get left behind by battles.
You can also sometimes recover items from Remnant Nexus stations.

All of this randomly generated at the start of the game, and will be fixed for that entire game.

Is it possible to NOT get all the enhancements in one run?

Also yes.
Very likely confirmation bias on my part, but it sometimes feels like the game 'favours' one particular item to shower you with, while others remain elusive.

Can you get some of the enhancements from quests, bar missions etc?

Yes.
There will be a character "with a paper book" lurking in a bar eventually, and they can offer such things for a price.
4 story points for the first one, 8 for the second, etc.

[FrancisJohn]

Thanks very much for all the responses, have compiled the lot together below so it's all in one spot.

Places you can raid
Pristine Nanoforge Chicomoztoc, in the Aztlan Star System (Hegemony) Kazeron, in the Thule Star System (Persean League)
Sindria and Natchiteka have Synchrotrons.
Eventide has a Spool.

Items are randomly generated with the map and repeating the same seed you will find the same items, though items you find though missions can vary.
Derelict Motherships can drop a forge as part of its loot.
Derelict motherships will often give items, and survey ships can sometimes also drop them.
You can find some colony improvements as random loot on core worlds you saturate bombard to death, but only if they have ruins. Effectively they are just ruins.
Abandoned Mining stations frequently give them, Research stations sometimes, and Habitats never.
It is also possible (although v. uncommon) to find items within abandoned ships - although these must be the ships that are 'generated' by the procgen, not the drifting ships that get left behind by battles.
You can also sometimes recover items from Remnant Nexus stations.

The historian can offer (randomly selected) colony items after the player knows most or all of the blueprints.  Cost is four story points for the first colony item, and doubles for each subsequent item.