Mk/**java.mk: Convert bsd.java.mk to USES

The following features have been added or changed:
- Instead of USE_JAVA use USES=java. This defaults to
  USES=java:build,run if NO_BUILD is undefined. Else it defaults to
  USES=java:run
- Instead of USE_ANT=yes use USES=java:ant which also implies
  USES=java:build
- Instead of JAVA_BUILD=yes use USES=java:build. Does not imply run or
  extract
- Instead of JAVA_EXTRACT=yes use USES=java:extract does not imply
  build or run
- Instead of JAVA_RUN=yes use USES=java:run does not imply extract or
  build
- Instead of USE_JAVA=<version> use USES=java and JAVA_VERSION=<version>

Approved by: mat (portmgr), glewis
Differential Revision:  https://reviews.freebsd.org/D48201

biology/jalview: Fix build by using gradle-7.6.1 instead of gradle-8.0.1

The gradle upgrade seems to have broken jalview.

Reported by:	fallout

biology/jalview: Update 2.11.1.4 -> 2.11.2.5

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>

cleanup: drop support for EOL FreeBSD 11.X

Search criteria used:
- 11.4
- OSREL*
- OSVER*
- *_FreeBSD_11

Input from:
- adridg: devel/qca-legacy
- jbeich: _WITH_DPRINTF, _WITH_GETLINE, GNU bfd workarounds
- sunpoet: security/p5-*OpenSSL*

Reviewed by:	doceng, kde, multimedia, perl, python, ruby, rust
Differential Revision: https://reviews.freebsd.org/D32008
Test Plan: make index

biology/jalview: Fix build

When switching the build dependency from devel/gradle to devel/gradle6,
the build is accidentally broken. This attempts to revert part of the
change and fix build.

Fixes:		55044a2200a4c42b6b653349f0a65dfca3f96f36
Approved by:	lwhsu (mentor, implicit), portmgr (fix build)

devel/gradle6: New port

devel/gradle needs to be updated to 7.x, while some ports build failed
under the newer version, including:

- biology/jalview
- biology/igv

Updated them to use this devel/gradle6 until they officially support 7.x.
No functional changes for these ports.

Approved by:	lwhsu (mentor)

biology/jalview: Broken on 11

Also fix number of lines in pkg-descr, and replace space with tab.

Reported by:	fallout

Clean up some things

- Fix typos
- Remove duplicate variables
- Remove nop variables
- Clean up commented PORTREVISION
- Add missing USES

Reported by:	portscan

biology/jalview: Update 2.07 -> 2.11.1.4

Take maintainership.

all: Remove all other $FreeBSD keywords.

Remove # $FreeBSD$ from Makefiles.

Restrict to Java 8, since this doesn't compile with Java 11

PR:			251774

Clean up after java/openjdk6 and java/openjdk6-jre removal

java/openjdk6 support was removed from Mk/bsd.java.mk (r512662) and
java/openjdk6 and java/openjdk6-jre were removed from the ports tree
(r512663).  Now this patch completely removes remaining stuff from the
ports tree.

PR:			241953 (exp-run)
Reviewed by:		glewis
Approved by:		portmgr (antoine)
Differential Revision:	https://reviews.freebsd.org/D22342

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

Approved by:	portmgr blanket

Remove $FreeBSD$ from patches files in categories a-j.

With hat:	portmgr
Sponsored by:	Absolight

Cleanup plist

Fix properties on pkg-plist

Support stage

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

Decommissioning java 1.5 (EOLed since October 2009):
suppress any reference to USE_JAVA=	1.5+ (part1)

- Reassign to the heap at maintainer's request

Now that the Java 1.3 and Java 1.4 ports are deprecated and will expire soon,
remove support for them from bsd.java.mk.  As Jikes is not available in Java 1.5
or higher, remove it from bsd.java.mk too (suggested by hq@) and from the ports
which used it (only occurences were USE_JIKES=no).  Support for the Blackdown VM
is also removed, as it is not available in Java 1.5 and higher.

Also remove the mapping from Java 1.1-1.4 to Java 1.5+ in bsd.java.mk to detect
old, broken ports; therefore bump the minimal value of JAVA_VERSION to 1.5.
While here, replace static values of JAVA_VERSION in files/*.in by
%%JAVA_VERSION%% .

PR:             ports/158969
Submitted by:   rene
Tested on:      pointyhat-west -exp

- Get Rid MD5 support

Bump portrevision due to upgrade of devel/gettext.

The affected ports are the ones with gettext as a run-dependency
according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT
in Makefile (29 of them).

PR:             ports/124340
Submitted by:   edwin@
Approved by:    portmgr (pav)

- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.

Jalview is a multiple alignment editor written in Java. It is used widely in a
variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain
database) and is also available as a general purpose alignment editor.

WWW: http://www.jalview.org

PR:             93054
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>