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The man page is just the --help output as reformatted by help2man. The --help option is most likely to change when the flex skeleton changes or one of the option parsing files changes or the configure.ac script itself changes. The dependencies reflect this now. It is still necessary, under some circumstances, to rebuild flex explicitly before building the man page. In theory, it's possible to have automake arrange to do this all the time, but doing so works out to be fragile, given the rest of the build system.