Fix ClassMapGenerator unambiguousReference test coverage

Without this fix the test only covers having files in "test", the "fixture"
portion it is not covered at all, because all fixtures in phpunit tests
are already in "test" directory
Avoid ambiguity warning for example directories as well

In particular, PEAR repositories use a classmap and example directories trigger
multiple false positive warnings.
Merge pull request #2895 from SlikNL/classmap-warning-example

Improve ambiguity warning test coverage and avoid ambiguity warning for example directories