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And refactored a few names/comments

this is useful so that loggers are all setup during tests

This set of commits implements the bootstrap commands,
following from the description in #117

- should not be on init, because need debug flag

Removed config.Filename and replace it with config.GetConfigFilePath that
takes a configuration directory as argument instead. Makes code simpler.
ipfs.getConfigDir now also return the default configuration dir instead of
an empty string in some cases.