I know a swap comes with axles, but does it come with the intermediate (half shaft?) shaft? and does the clutch slave cylinder come attached to the tranny?

 

the majority of places yes the clutch slave cylinder is included...but you can use your stock one.
and yes the IS is included for 99.99% of places.

most the time when you hear "full swap" it has everything your gonna need.

 

yea most swaps come with them mine did

 

are all clutch slave cylinders the same? will an integra one work with the civic clutch master cylinder?

 

Here in L.A., i've heard junk yards use the term "conversion kit" when talking about all the items needed for an engine swap. I like this term due to it being clear that you are not just swaping in a similar engine and will need all the parts required for the conversion.

Wes V