Avoid reading twice header-vars.am as now macro_define

Avoid reading twice header-vars.am as now macro_define
complains.
* automake.in (&define_standard_variables): Don't output the
variables.
(&read_main_am_file): Output first user variables, then Automake
variables.
Don't call twice &define_standard_variables.
Save variable comments in $am_vars.
(&variable_output): New.
(&file_contents_internal): New.
Save variable comments in $am_vars.
(&file_contents): Use it.