fix duplicate documents and tests for add/remove files to index
this fixes #7
Fix srcdir for the jrcs build target.

Since the old srcdir was a parent of the actual source root, Ant got
confused and always rebuilt jrcs, also in incremental builds when
jrcs hadn't been changed. Now, incremental builds will only rebuild
it if something has changed in the jrcs code.
attempt at ignoring paths, by using pattern matching on file.getAbsolutePath(), instead of file.getName()
Merge branch 'master' of github.com:cnst/OpenGrok