pmd: fix #1081 Regression: CPD skipping all files when using relative paths
pmd: fix #1082 CPD performance issue on larger projects
pmd: adding more entries to gitignore and to exclude while creating the source zip file.
pmd: fix #1080 net.sourceforge.pmd.cpd.CPDTest test failing
The symlinks are simply removed now from the source code and
created by the test, when needed.
The test runs only under unix systems, not under windows.