biology/sra-tools: Update to 3.1.1

Numerous fixes and enhancements since 3.0.6
Changes: https://github.com/ncbi/sra-tools/commits/master/

All previous patches upstreamed
Rewrote pkg-descr to be more introductory

biology/sra-tools: Quick fix to unbreak build

jquery version in pkg-plist changed, not sure why
Port is due for upgrade anyway

cleanup: remove occurrences of WITH_DEBUG

DEBUG like all ports features, must not ever be set in a port, they are
user facing features, that the user needs to enable in their
environment/make.conf, either by defining WITH_DEBUG globally, or by
setting WITH_DEBUG_PORTS with origin of ports they want DEBUG enabled
in.

biology/sra-tools: Update to 3.0.6

Major code and build system rework since 2.11
Now supports aarch64, unblocking rna-seq and atac-seq metaports
Changes: https://github.com/ncbi/sra-tools/commits/master

Reported by:    portscout

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

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.

science/hdf5: bump PORTREVISION of consumers

The SO-version increased in the update to 1.12.2 in
a43418b81530f7e897abfbe18dd59f44265a1a0f .

Reported by:	VVD <vvd@unislabs.com>

biology/sra-tools: Fix build with HDF5 1.12.0+

textproc/libxml2: bump all LIB_DEPENDS consumers

This is a separate commit to facilitate easier cherry-picking for
quarterly.

PR: 262853, 262940, 262877, 263126
Approved by: fluffy (mentor)

textproc/libxml2: bump all dependencies

This should make sure that all dependent ports will pick
up the new version commited with a13ec21cd733f67a9fc0dc00ab45268bdc236246

Fix CONFLICTS entries of multiple ports

There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.

This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.

Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port

biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read
Archives

SRA tools is a toolkit for using data in the INSDC Sequence Read Archives.

SRAs operated by International Nucleotide Sequence Database Collaboration
houses sequence reads and alignments generated by "next-gen" sequencers.

This port is a bit convoluted due to the fact that the sra-tools build
requires access to the ncbi-vdb source tree.  Hence, ncbi-vdb is treated
as a submodule here rather than a separate library port.  We are working
with upstream with hope for long-term improvements.