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Yes, that should work. You have the class abilities to trade out. Also see a post by James Jacobs here:
http://paizo.com/threads/rzs2l7ns&page=330?Ask-James-Jacobs-ALL-your-Qu estions-Here#16471

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Unknown. I'd ask around locally.
My opinion is yes. They were described as giant archtypes. it was stated that ninjas ARE rogues. part of the book alternate classes in explicitly stated that they were a really big archetype...
but paizo went so far as to edit that part of the book out. They may have something different in mind for alternate classes and the like. Clarification is pretty far down the priority list though.

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These are standalone classes whose basic ideas are very close to established base classes, yet whose required alterations would be too expansive for an archetype
and
An alternate class operates exactly as a base class, save that a character who takes a level in an alternate class can never take a level in its associated class
Ninja is a standalone class that isn't allowed to multiclass with Rogue. As a standalone class, it's not able to take Rogue archetypes

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Ultimate Combat - Alternate Classes wrote:These are standalone classes whose basic ideas are very close to established base classes, yet whose required alterations would be too expansive for an archetypeand
Quote:An alternate class operates exactly as a base class, save that a character who takes a level in an alternate class can never take a level in its associated classNinja is a standalone class that isn't allowed to multiclass with Rogue. As a standalone class, it's not able to take Rogue archetypes
an alternate class (ninja) functions exactly as a base class (rogue). A base class can take archetypes.

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... designed for that base class. The Ninja can take any ninja archetypes there are, of course. ;)
It's definitely a grey area, unlikely to be resolved until Paizo resolves it. So, for PFS, keep in mind that you might find GMs who allow it, and those who don't. Until Paizo rules, they're both right. Unfortunate, but true.
It does look like they're stepping back from the "big archetype" idea and moving to the "stand-alone class" idea, which to me means that there's a whole book of ninja archetypes waiting to be designed...

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... designed for that base class.
That's not what it says. Archetypes are designed to worth with other archetypes if they still have the same class features. Furthermore
- Alternate classes are really just expanded archtypes. The distinction is that for an alternate class, we represent all of the rules needed to run the class. It is similar to its base, but has a significant number of swaps. There are certainly some archtypes that could have received this treatment, but we chose to leave them as more abbreviated write ups. Linky
Originally, the ninja was no more a different base class than the rogue than The Dawnflower Dervish was a different class than the bard , to the point that many existing archetypes could have been written up as base classes instead with no change other than paizo doing the shopandswap math for you.
It does look like they're stepping back from the "big archetype" idea and moving to the "stand-alone class" idea, which to me means that there's a whole book of ninja archetypes waiting to be designed...
and only one that they've made (seemingly after the shift)

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The quote from Jason B is from 2011, so I went and checked the current printing of Ultimate Combat. Here's what it says in its entirety (emphasis mine):
Alternate Classes
These are standalone classes whose basic ideas are very close to established base classes, yet whose required alterations would be too expansive for an archetype. In this case, that’s the samurai and the ninja—specifically Asian-themed classes that have long and unique histories, as well as great cultural cachet, but which are similar in concept to the established cavalier and rogue, respectively. An alternate class operates exactly as a base class, save that a character who takes a level in an alternate class can never take a level in its associated class—a samurai cannot also be a cavalier, and vice versa. The antipaladin from Advanced Player’s Guide is also an alternate class.
Note that it doesn't say "an alternate class operates exactly as the base class it was based on"... it says that (any) alternate class operates like (any) base class. An alternate class can be taken by a new character, has no prerequisites, can multi-class (except with the base class it was based on), can take archetypes designed for that (standalone) class, it can go up to 20 levels, etc. just like a base class (and differently from say a prestige class).
Based on this, it seems clearer (to me, anyway) now that ninjas can't take rogue archetypes any more than fighters can.

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There are many Ninja (Scouts) running around in PFS. They were explicitly legal at one point, and people who ran into table variation then carried with them the proper supportive quotes.
Then Pathfinder Unchained was released, and some weird statements were made about the Ninja that went against the current understanding. Many threads were created asking for clarification, and all we got from the newest member of the Paizo team was "It will be changed".
Currently, at best, it's unclear whether Ninjas can be Scouts. I have a level 8 Ninja (Scout) that I've been forced to shelve until the issue gets resolved. And if it gets resolved against Ninjas taking archetypes, then he'll just get thrown in the garbage.
I have other characters that are currently legal that I'd rather enjoy before they get arbitrarily changed.

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Base class is the term used for non-core and non-themed classes. Alchemist, summoner, oracle, and magus are all base classes. So a ninja is a base class in that it is a a PC class that is meant to be used along with the core classes.
This is further supported by them using "associated class" instead of base class. Because base is like cavalier, and associated is the ninja can't multi-class with rogue.
so officially, they can't, as they are their own separate class and nothing says they can. Thing is, this is new clarification and many don't like it and it's a reversal so many people were doing it already. And unofficially, if they ever clarified this they'd possibly allow it.

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Not on archives of nethys yet, but I was surprised to find a Ninja specific archetype in one of the newer supplements. I think it was inner sea intrigue, but I could be wrong. Wasn't super impressive, but it was snow themed ninja archetype that was native to the inner sea, rather than the distant shores.