When profiling a complex script, is there any way to only get results that are in the currently selected project? When I profile, most of the top 30 lines are Smarty things. I don't mind Smarty function calls in my project (the Smarty require() is the single slowest line), but it shouldn't profile within libraries unless they are part of the project or workspace.

(I don't know if this is an IDE or a debugger issue, sorry if it's the wrong place.)

Profiler should profile script execition, therefore it should count time spent in php engine, php extensions, libraries and any other scripts involved in the execution.
If for any reason you need a particular line in the results to be excluded, just press [-] button. You can also select multiple lines, press [-], and exclude them all at once. Not a big deal.

It should certainly count the time, but the results shouldn't tell me about some little private method deep in Smarty unless I specifically ask to see those results. They can be removed but it's very fiddly to find and remove rogue entries every time.