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By the way I think there is a typo in one the commands above. I think you meant to write config -a index.exclude /opt/local instead of config index.exclude -a /opt/local. The latter will cause the default exclude path of /usr to be replaced with .../-a and /opt/local. This means everything in /usr is indexed.
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I would expect the clang-tags config command to work in all cases, whether -a is placed before or after the option name. The commands above are the actual ones that I used, and it did work as expected (at $WORK with python 2.6.6, i.e. without the newer argparse module). I'll check whether I can reproduce your bug for newer python versions with argparse.
From issue #8:
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