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HBSD: Resolve merge conflict

Signed-off-by:  Shawn Webb <shawn.webb at hardenedbsd.org>

Merge remote-tracking branch 'internal/freebsd/main' into hardenedbsd/main

Conflicts:
        sysutils/pv/Makefile (unresolved)

math/libsemigroups: upgrade to 2.3.2

Note: the latest release is v2.7.3, but 2.3.2 is the one needed for Sage.

math/hpcombi: upgrade to 1.0.1

Releases notes at <https://github.com/libsemigroups/HPCombi/releases>.

math/py-cypari2: upgrade to 2.1.5

Releases notes at <https://github.com/sagemath/cypari2/releases>.

sysutils/pv: Update to 1.8.9

Changelog:
https://codeberg.org/a-j-wood/pv/src/tag/v1.8.9/docs/NEWS.md

Port changes:
- Use SSL for MASTER_SITES
- Change license from ART20 to GPLv3+
- Remove obsolete option LFS
- Switch to using a pkg-plist file

PR:     278528
Reported by:    kunda <luzpaz at pm.me>

security/whatweb: add missing run dependency

PR:             278502
Reported by:    runtomaker at gmail.com
Submitted by:   maintainer

textproc/py-csvkit: update to 2.0.0

Changes:        https://github.com/wireservice/csvkit/blob/2.0.0/CHANGELOG.rst
Reported by:    portscout, repology

net/dhcpd: fix build on 15-CURRENT

PR:             275313
Reported by:    Mallorya at fastmail.com
Submitted by:   maintainer

Revert "www/chromium: Change default audio output to PULSEAUDIO to make chromium to play nice with desktop environments"

This reverts commit 89e432ced730385869e5bf6df4b705facbd1c947.

Reason: Several people complained that the PulseAudio dependency is a lot heavier than Sndio.

This is currently a controversial issue because:
1. PulseAudio is indeed a heavier dependency compared to Sndio,
   so for people who prefer minimalistic setup Sndio should be a default.
2. Currently desktop environments work best with PulseAudio, so
   it is better for average users to have PulseAudio as a default backend.

It would be best if www/chromium would allow to change audio backend at-startup
or on-the-fly without the need to change port options.

This can be achieved by the following methods:
1. Flavorizing www/chromium based on audio backends.
2. Creating slave ports with different audio backends.
3. Implementing on-the-fly or at-startup setting of the audio backend.

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math/topcom: update 0.17.8 → 1.1.2

PR:             278778 (addition of EXTRACT_AFTER_ARGS)
Submitted by:   Daniel Engberg <diizzy at FreeBSD.org> (addition of EXTRACT_AFTER_ARGS)

math/{,py-}topologic: update 0.6.0 → 6.0.2

Reported by:    portscout

biology/star: Use EXTRACT_AFTER_ARGS to omit unused htslib dir

Reduces I/O during builds

PR:             278751
Reported by:    diizzy

biology/kallisto: Use EXTRACT_AFTER_ARGS to omit unused htslib dir

Reduces I/O during builds

PR:             278739
Reported by:    diizzy

net/benthos: Add new port

Benthos solves common data engineering tasks such as transformations,
integrations, and multiplexing with declarative and unit testable
configuration. This allows you to easily and incrementally adapt your data
pipelines as requirements change, letting you focus on the more exciting stuff.

Benthos is able to glue a wide range of sources and sinks together and hook
into a variety of databases, caches, HTTP APIs, lambdas and more, enabling you
to seamlessly drop it into your existing infrastructure.

sysutils/limine: Update to 7.5.0

changeLog:
https://github.com/limine-bootloader/limine/releases/download/v7.5.0/ChangeLog

PR:             278723
Approved by:    submitter is maintainer

textproc/cl-ppcre-sbcl: update to version 2.1.2

textproc/cl-ppcre: update to version 2.1.2

sysutils/tflint: Update to 0.51.0

changeLog:
https://github.com/terraform-linters/tflint/releases/tag/v0.51.0

sysutils/bacula15-server: Fix broken S3 option

I did not properly convert the S3 option from the old format to the
new format.

PR:             278312

Merge branch 'freebsd/main' into hardenedbsd/main

biology/pbseqan: Remove expired port

2024-05-05 biology/pbseqan: Upstream merged into SeqAn project: Use biology/seqan

net/haproxy-devel: update to version 3.0-dev10

devel/R-cran-mlbench: Update to 2.1-5

ChangeLog: https://cran.r-project.org/web/packages/mlbench/NEWS

devel/R-cran-kit: Update to 0.0.17

ChangeLog: https://cran.r-project.org/web/packages/kit/news.html

devel/aws-c-io: Update to 0.14.8

ChangeLog: https://github.com/awslabs/aws-c-io/releases/tag/v0.14.8

misc/bedrust: New port: Invoke NN models on Amazon Bedrock

net/torsocks: Fix USE_LDCONFIG

devel/bacon: update 2.16.0 → 2.17.0

Reported by:    portscout

misc/llama-cpp: update 2784 → 2789

Reported by:    portscout