Analysis will always include all code. Why? Why take the time to analyze all of it when only a file or two has been changed? Because any given change can have far-reaching effects. I’ll give you two examples:
I check in a change that deprecates a much-used method. Suddenly, issues about the use of deprecated code should be raised all over the project, but because I only analyzed that one file, no new issues were raised.
I modify a much-used method to return null in some cases. Suddenly all the methods that dereference the returned value without first null-checking it are at risk of NullPointerExceptions. But only the one file that I changed was analyzed, so none of those “Possible NPE” issues are raised. Worse, they won’t be raised until after each individual file happens to be touched.
And that’s why all files are included in each analysis.