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Running on OpenBSD, I issue a:

git clone https://github.com/openbsd/src.git

then how can I compile all the OpenBSD binaries? Is there a "master" make file? I only need the binaries inside the src directory, not in place like /bin etc.

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Compiling OpenBSD's base system is described in the OpenBSD FAQ under the section Building the System from Source.

It is assumed that you build the system with an OpenBSD system that is recent and that you have an up-to-date kernel installed and have read the Following -current FAQ.

The "master" Makefile is the Makefile in the top of the src hierarchy.

Building the base system is not allowed with DESTDIR set (this is disallowed in the main Makefile), so you can't really build the system and install in an alternate location that way, and the install target is built by default.

I would suggest building the base system in a chroot (which I haven't tried) or in a virtual machine.

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