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Merge build/make/deps into build/make/Makefile.in #29098

@mkoeppe

Description

@mkoeppe

The split between these two files seems arbitrary, and after many changes to the build system, the naming of the file deps is no longer meaningful. We merge the two files.

Depends on #28000

CC: @dimpase @embray @jhpalmieri @orlitzky

Component: build

Author: Matthias Koeppe

Branch/Commit: e1a9413

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/29098

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