lib/sh/util.sh: auto-echo common external commands: use simpler echo_run instead of command since logging handling is not needed

added backups/vegbien.r9897.backup.md5

lib/sh/sync.sh: upload(): documented that each --include path is relative to the currdir, not the root dir of the upload ($local_dir). this feature, although previously unintended, is actually better because the user can change to a subdir of the root dir and specify upload paths relative to the dir they are in. however, when invoking upload() from a script with --include paths specified, this means you need to use an absolute path (e.g. "$(dirname "${BASH_SOURCE⁰}")"/...; or the value that will become $local_dir, which for sync_upload() is $root_dir).

backups/.rsync_ignore: replaced with .rsync_filter.upload to allow uploading new backups but not deleting existing backups if they don't exist on the local (rsync-invoking) side; and .rsync_filter.download to avoid downloading backups to the local side. this allows storing older backups just on jupiter, where there is much more disk space. note that this change must be made on the remote side (jupiter) for it to be effective, because these are remote-side rules and are only processed by the remote-side rsync instance.

lib/sh/sync.sh: upload(): use directional .rsync_filter to supplement .rsync_ignore with all kinds of --filter rules. separate .rsync_filters are needed for the upload (swap=) and download (swap=1) directions because the sender and the receiver are reversed, causing asymmetric rules like protect/hide to change meaning.

updated backups/TNRS.backup.md5

added backups/TNRS.2013-6-17.backup.md5, TNRS.2013-6-22.backup.md5

/README.TXT: Backups: TNRS cache: Back up/Restore: added runtimes (3 min/5.5 min)

lib/sh/sync.sh: upload(): usage: documented put's swap=1 flag, which downloads instead of uploads

added inputs/GBIF/raw_occurrence_record_plants/.rsync_ignore with filters that have previously needed to be manually added whenever `make inputs/upload` was run