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testing with autotools

 Gentoo Mono Handbook, testing with NUnit
 
make check
tests the files in the source tree
make installcheck
tests the installed copies

checking a specific directory

http://stackoverflow.com/a/8422390/6017919

if you only wanted to check in a specific directory, override check-recursive target in your Makefile.am:

check-recursive:
    $(MAKE) -C src check