run-autotools is run after pre-configure

[Alejandro Pulver]

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Hello.

I am creating a port (devel/allegro-devel, based on devel/allegro)
which uses autoconf 2.59. I need to replace "-lpthread" with
${PTHREAD_LIBS} to make it work on FreeBSD 4.x, but autoconf is
executed after patching so it overwrites the configure script.

I could deal with this by redefining run-autotools, but I think that's
not recommended.

Should run-autotools be done before pre-configure to allow patching it?

Best Regards,
Ale
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