Please read the documentation http://www.jacoco.org/jacoco/trunk/doc/
There is "Merge" Ant Task ( 
http://www.jacoco.org/jacoco/trunk/doc/ant.html ), "Merge" Maven Goal 
( http://www.jacoco.org/jacoco/trunk/doc/merge-mojo.html ) and not yet 
released "Merge" command in command line interface ( 
http://www.jacoco.org/jacoco/trunk/doc/cli.html ).
All code of their implementation is available - 
https://github.com/jacoco/jacoco
Please note that execution data is merged only for the same classes ( 
http://www.jacoco.org/jacoco/trunk/doc/classids.html ), i.e. common classes 
used by your Application A and by Application B should be the same and 
exact same classes should be used during creation of a report.

On Saturday, July 22, 2017 at 7:20:05 PM UTC+2, Andrew Iyer wrote:
>
>
> I have four applications that run using the same codebase.
>
> I have instrumented all of them successfully.
>
> The problem is that Application A uses half of the codebase of package X, 
> and Application B uses the *other* half of package X.
>
> So, for example, one Application will call the "initialize" function, the 
> other application will be sent this, say, and then call the "toString" 
> function to save it to a db.
>
> When I look at my jacoco report, given this pattern of usage, I see only 
> an average of 20% coverage, whereas I suspect the *actual* coverage is 
> closer to 60%.
>
> I'm using (pretty much, the code sample isn't complete but you get the 
> idea) the same code from here:
> https://stackoverflow.com/a/31250878/1061426
>
> thanks
>

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