biology/migrate: fix build on !x86

biology/migrate: Use system zlib instead of excluding it from extract

Fixes:		dc29da5db6e6e: Fix extract on aarch64

biology/migrate: Fix distinfo

Upstream re-rolled tarball.

biology/migrate: Update to 5.0.6

ChangeLog: https://peterbeerli.com/programs/migrate/distribution_4.x/HISTORY

biology/migrate: Fix extract

Extract fails on aarch64 with error:
(sample)
"dynsections.js: Cannot restore extended attributes:
com.apple.quarantine com.apple.quarantine: No such file or directory"
tar: Error exit delayed from previous errors.-

Fix extract with: --no-same-owner --no-same-permissions

biology/migrate: Update to 5.0.5

- Switch to DISTVERSION
- Add license
- Pet portlint, portclippy and portfmt
- Take maintainership

ChangeLog: https://peterbeerli.com/programs/migrate/distribution_4.x/HISTORY

MAN[1-5]PREFIX: eleminate its usage  and move man to share/man

Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)

Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>

Update CONFLICTS definitions in categories a* to c*

Update the CONFLICTS definitions of ports in the following categories:

- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters

An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.

There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.

Approved by:	portmgr (implicit)

Remove # $FreeBSD$ from Makefiles.

Mark BROKEN on riscv64 the same as armv*:

  # make[2]: cannot open makefile..

Note the filname reported is "Makefile." (e.g. probably empty suffix).

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com build testing

Mark broken on armvX and mips.

- Switch to options helpers
- Regenerate patches with `make makepatch`
- Simplify plist

- Update options

- Update to 3.6.11
- Convert to optionsNG

- Update to 3.6.9 and unbreak

Mark as broken unfetchable ports

Upgrade from 3.6.6 to 3.6.7. Be sure to not extract the zlib
subdirectory.

6 ports categories: Remove $PTHREAD_LIBS

Categories: cad, devel, java, x11-fm, biology, deskutils

approved by:	PTHREAD blanket

- Update to 3.6.6

PR:		197039
Submitted by:	antont@inbox.lv

- Update to 3.6.5
- Reset maintainer to ports@

- Stagify; cleanup Makefile and reorder the knobs a bit
- Drop the case for long unsupported alpha architecture

Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)

- Update to 3.5.1
- Trim Makefile headers
- Convert to optionsNG
- Update WWW, MASTER_SITES and COMMENT

Update MASTERSITES for my server to use https

Approved by:	wen (maintainer, implicit)

- Get Rid MD5 support

- Take maintainership

- Reassign to the heap

PR:             ports/155507 ports/155508

- Add an additional MASTER_SITES

PR:             ports/151112
Submitted by:   gjb (maintainer)
Approved by:    pgollucci (mentor)

- Update MAINTAINER to submitters new mail address

PR:             ports/150274
Submitted by:   Glen Barber <glen dot j dot barber at gmail dot com>
(maintainer)
Approved by:    beat (co-mentor, implicit)

- Update to 3.1.6

PR:             ports/147194
Submitted by:   Glen Barber <glen.j.barber@gmail.com> (maintainer)

- Update to 3.1.4

PR:             ports/146411
Submitted by:   Glen Barber <glen.j.barber@gmail.com> (maintainer)

- Update to 3.1.3
- Pass maintainership to submitter

PR:             ports/144992
Submitted by:   Glen Barber <glen.j.barber@gmail.com>

Update to 3.1.2

- Update to 3.1.1

PR:             143437
Submitted by:   Ports Fury

For ports maintained by ports@FreeBSD.org, remove names and/or
e-mail addresses from the pkg-descr file that could reasonably
be mistaken for maintainer contact information in order to avoid
confusion on the part of users looking for support. As a pleasant
side effect this also avoids confusion and/or frustration for people
who are no longer maintaining those ports.

- Update to 3.0.3

PR:             130459
Submitted by:   KATO Tsuguru <tkato432@yahoo.com>

- File was rerolled for a small bugfix.

Submitted by:   pointyhat via pav/erwin

- Update to 2.4.3

Submitted by:   Ports Fury

- Update to 2.4.2 (fix fetch problems)

Submitted by:   pointyhat via pav

- Update to 2.4.1

PR:             119719
Submitted by:   KATO Tsuguru <tkato432@yahoo.com>

- Update to version 2.3

PR:             ports/116019
Submitted by:   KATO Tsuguru

- Update to 2.1.3
- Fix fetching
- Remove old patch and use MAKE_ARGS instead
- portlint(1) and whitespace

Approved by:    erwin (mentor)

Remove USE_REINPLACE from all categories starting with B

- Add SHA256

At Kris's request, back out the MACHINE_ARCH spelling correction until
after 5.4-RELEASE.

Assist getting more ports working on AMD64 by obeying the
Ports Collection documentation and use 'ARCH' rather than 'MACHINE_ARCH'.

Fix build on 4.x

PR:             ports/77697
Submitted by:   Sam Lawrance <boris at brooknet.com.au>

Update to version 2.0.3

PR:             ports/77676
Submitted by:   Sam Lawrance <boris at brooknet.com.au>

With portmgr hat on, reset maintainership of this port.  All of wjv's
other ports were reset a couple of months ago; this one appears to have
been missed.

Update to 1.7.6.1.

PR:             ports/67429
Submitted by:   Roman Neuhauser <neuhauser at chello dot cz>
Approved by:    maintainer timeout (4 weeks)

SIZEify (maintainer timeout)

BROKEN on alpha: Does not compile

Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:   Oleg Karachevtsev <ok@etrust.ru>
A part of PR:   57992

Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.

- Update to version 1.2.4    

Correct my email address.    

Add migrate 1.2,   a program to estimate population sizes and   migration rates.