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I have a Makefile.am file in my source folder and some makefile.in in some subdiretories. Everything works fine but I’ve noticed that when I do a make dist the tarball doesn’t include the makefile.in in the subdirectories. Also because of this, make distcheck fails.
I believe the only way this can happen is if you fail to specify the subdirectory is a SUBDIRS clause of the appropriate higher level Makefile.am, although it seems strange that ‘everything works fine’ if that is the case. Unless you are actually naming the
makefile.inwith a lower casem, in which case you would need to add that file toEXTRA_DIST, but the better solution would probably be to use the standard name with upper-caseM.