How do you identify an alchemist's extract being used in combat? Is it knowledge for identifying a class feature, spellcraft for a spell? Is the spell being cast or used etc?
You cannot identify alchemist's extracts being used in combat
Alchemy (Su): Alchemists are not only masters of creating mundane alchemical substances such as alchemist’s fire and smokesticks, but also of fashioning magical potion-like extracts in which they can store spell effects. In effect, an alchemist prepares his spells by mixing ingredients into a number of extracts, and then “casts” his spells by drinking the extract.
Note the quotes on "cast"? Yes, they are not actually casting spells, so any method of identification based on spells being cast, such as Spellcraft, will fail against extracts. All the relevant preparations were done when those extracts were created, and all the alchemist has to do is drink them for their effects to take place.
Extracts are the most varied of the three. In many ways, they behave like spells in potion form, and as such their effects can be dispelled by effects like dispel magic using the alchemist’s level as the caster level. Unlike potions, though, extracts can have powerful effects and duplicate spells that a potion normally could not.
Extracts duplicate spells but are not spells. That said, it is weird that they say that extracts behave in many ways like spells, but only list one exception that applies to spells and not to supernatural abilities: be dispellable.
However, you can identify the school of magic by observing the magic effect created by an extract using Knowledge (Arcana) with a DC 15+spell level, or identify the exact spell effect caused by an extract using Knowledge (Arcana) with a DC 20+spell level.
You can also identify that the alchemist drank an extract instead of a regular potion (or even a bottle of water) using Knowledge (Local) with a DC 11 (10 plus 1, the level alchemists gain their extracts as a class ability).
In my research I've found that one out of three methods seems to be the most accurate one. Alchemist extracts is a supernatural class feature that imitates a mix between potions and spells.
Method 1: Spellcraft to identify a spell being cast. DC 15+Spell level
Method 2: Knowledge(arcane) to identify a spell effect that is in place. DC: 20+spell level.
Method 3: Knowledge(arcane), to identify a class feature.
Method one is supported by the faq released in October 2015. Method two and three are supported by ultimate intrugue as well as the core rulebook in of spellcraft.
Although this isn’t directly stated in the Core Rulebook, many elements of the game system work assuming that all spells have their own manifestations, regardless of whether or not they also produce an obvious visual effect, like fireball. You can see some examples to give you ideas of how to describe a spell’s manifestation in various pieces of art from Pathfinder products, but ultimately, the choice is up to your group, or perhaps even to the aesthetics of an individual spellcaster, to decide the exact details. Whatever the case, these manifestations are obviously magic of some kind, even to the uninitiated; this prevents spellcasters that use spell-like abilities, psychic magic, and the like from running completely amok against non-spellcasters in a non-combat situation. Special abilities exist (and more are likely to appear in Ultimate Intrigue) that specifically facilitate a spellcaster using chicanery to misdirect people from those manifestations and allow them to go unnoticed, but they will always provide an onlooker some sort of chance to detect the ruse.
I answered the own question after reading more of the forums, if anyone has anything to add, please add a comment or your own answer, I'm happy to be given more information on the topic, rules, developer statements, errata, rules etc is great.