Import patches from FreeBSD port

[outpaddling]

This fork contains all the patches necessary for the FreeBSD port, and lays the foundation for porting to other BSDs. Since most of the OS checks were alphabetized, I also took the liberty of reorganizing those that we not.

[klymenko]

@outpaddling, how did you build it?

[outpaddling]

Using the FreeBSD ports system. This is how virtually all software is installed on FreeBSD.

My work-in-progress ports collection contains the latest:

https://github.com/outpaddling/freebsd-ports-wip

The "sra-tools-fork" port uses this fork, so the port framework has to do minimal patching (see the REINPLACE_CMDs in the port Makefile). The regular "sra-tools" port contains all of the patches in this fork in the files directory, and applies them automatically after the dist is extracted.

For NetBSD and other POSIX systems (including RHEL and macOS), I use pkgsrc, which is derived from FreeBSD ports.

[klymenko]

@outpaddling, this PR was merged into engineering branch, as well.

[outpaddling]

Yeah, I saw that. FYI, I'm updating the pkgsrc package now and the NetBSD build caught one more missing header in the latest engineering commit.

--- ncbi-vdb/libs/kdbtext/path.hpp.orig 2024-03-21 22:06:49.815904250 +0000
+++ ncbi-vdb/libs/kdbtext/path.hpp
@@ -28,6 +28,7 @@
 
 #include <string>
 #include <queue>
+#include <cstdarg>
 
 #include <klib/rc.h>

[klymenko]

This pull request was merged.