Remove # $FreeBSD$ from Makefiles.

biology/clustalw: Fix license, take maintainership

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15503

Remove useless WRKSRC definitions.

While there, correct DEV_WARNINGS when they occur.

Sponsored by:	Absolight

- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket

MASTER_SITES cleanup.

- Replace ${MASTER_SITE_FOO} with FOO.
- Merge MASTER_SITE_SUBDIR into MASTER_SITES when possible. (This means 99.9%
  of the time.)
- Remove occurrences of MASTER_SITE_LOCAL when no subdirectory was present and
  no hint of what it should be was present.
- Fix some logic.
- And generally, make things more simple and easy to understand.

While there, add magic values to the FESTIVAL, GENTOO, GIMP, GNUPG, QT and
SAMBA macros.

Also, replace some EXTRACT_SUFX occurences with USES=tar:*.

Checked by:	make fetch-urlall-list
With hat:	portmgr
Sponsored by:	Absolight

Multiple ports: reset maintainers
	Maintainers for these ports have been notified on 5 separate occasions
	over the course of several months about pending actions required.

	We really appreciate the time and effort you put in to maintain
	these ports.

	If you are still interested in helping to maintain these ports just
	reply to me or file a PR and I will happily assign the port to you
	again.

Approved by:	portmgr (implicit)

- Fix build with clang/libc++.
- Support staging.

PR:		184974
Submitted by:	tijl@

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

Remove USE_GNOME=gnometarget from ports. It has been a empty keyword since
mid 2008.

PR:             ports/159624
Submitted by:   Ruslan Mahmatkhanov <cvs-src@yandex.ru>

- Fix fetch

Reported by:    QAT@

- Update to 2.1

- Fix fetch error

- Update to 2.0.12
- Update my mail address to FreeBSD

- Update to 2.0.6
- Pass maintainership to submitter

PR:             123193
Submitted by:   Wen heping <wenheping@gmail.com>

- Update to 2.0.5
- Add RESTRICTED due to non-commercial use licence.

PR:             ports/121794
Submitted by:   KATO Tsuguru <tkato432@yahoo.com>
Approved by:    thierry and tabthorpe (mentors)

- Update to version 2.0.5
- Add RESTRICTED due to a non-commercial use licence.

PR:             ports/121794
Submitted by:   KATO Tsuguru <tkato432@yahoo.com>
Approved by:    thierry and tabthorpe (mentors)

- Restore clustalw symlink, other ports rely on it

Reported by:    pointyhat
Pointy hat to:  pav

- Update to 2.0.3

- Update to 2.0

PR:             ports/117713
Submitted by:   Motomichi Matsuzaki <mzaki@e-mail.ne.jp>

Reset dbader@eece.unm.edu due to maintainer-timeout.  While here, fix fetch.

SHA256ify

Approved by:    krion@

- Add an end-of-string to each line of the input
  when parsing the input files

PR:             56043
Submitted by:   maintainer

Update to 1.83.

PR:             48264
Submitted by:   David A. Bader <dbader@eece.unm.edu>

- Add a new patch
- Bump $PORTREVISION

PR:             36206
Submitted by:   David A. Bader <dbader@eece.unm.edu> (MAINTAINER)

- Fix certain mistakes in FreeBSD patches
- Bump PORTREVISION
- Poroblem originally reported by Fernan Aguero <fernan@iib.unsam.edu.ar> on
  FreeBSD-bio list

PR:             36169
Submitted by:   David A. Bader <dbader@eece.unm.edu> (MAINTAINER)

${PREFIX}/share/${PORTNAME} --> ${DATADIR}    

Update to version 1.82    

Convert category biology to new layout.  

- Support CC/CFLAGS/PREFIX properly   - gets() -> fgets()   - Add WWW: line into
pkg/DESCR    

Adding clustalw version 1.81.   A CLUSTAL W Multiple Sequence Alignment Program.