It was rhetorical - why not just use autoconf to do all the dirty work?

Like Lynn Ten Eyck says, autoconf configures dependences, it doesn't build them (AFAICS, anyway).

Also, is the idea to migrate all of the scripting away from guile and
towards python,

No.

or update the guile dependencies (as it seems goosh is
part of the os process module now,

OK, Noted.

guile-gtk is deprecated in favor of
guile-gnome,

I've not heard that.

guile net-http and guile-gui look unsupported...)?

Yes, they are tiny packages that could easily subsumed into Coot itself for ease of packaging (as Bill Scott once suggested). Not done, no-one complained enough.

 I'd
like to begin preparing a rpm for fedora (now that most of the
dependencies are part of the distributions),

Good going! MATSUURA Takanori and Adam Huffman said they'd like to do something similar.

but their peer review
process might screen out unsupported deps...

Hmm... Fingers crossed we'll get the mmdb license issues sorted soon.

Paul.

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