fix sql for Fido FPR command

refs #7244

sql used to create FPR command for Fido on upgrades from 1.1.0
did not have spaces.
removing some delete statements from upgrade script

refs #7249
MicroServiceChainLinks cannot be deleted from an upgraded system
as there may be existing jobs that have foreign key links to those
MCSL's.

Rather than delete some MCSL's from an upgraded database, it seems
better to keep all upgraded systems in the same state.

This results in some orphaned MicroServiceChains, that do not
appear in a fresh install, but these orphaned Chains will not
be reachable, they will exist only to satisfy the foreign key
constraints (and provide context for the historical jobs data).
Update Software Agent code on upgrade

refs #7266

Change the Agent Code for software agent when upgrading by packages
from Archivematica 1.1.0 to 1.2.0
MCPClient: remove unused rfc6266 dependency

This was once used in Archivematica's email code, but was removed in
6d86d6add9fe516e8a806eeaf4eef2cb389e9447 and never used anywhere else
in the code.
Add move from TS to current pipeline helper

Add helper function to move files from a transfer source location to a
path on the current pipeline. To enable this, add the location UUID to
the browse JS.
Cleanup: get_temp_dir, whitespace, JS

Remove unused get_temp_directory. Fix whitespace in copy_to_start_transfer.
Use .get instead of try/except. Return early in JS. Hide in-progress
indicator when start transfer fails.
Start Transfer: Call SS to move files

refs #7151

Replace copy_transfer_component with calls to copy_to_start_transfer to get
the SS to move files. New transfers get staged to a temp dir in
sharedDirectory/tmp, then moved to the correct watched directory.

Update Javascript in directory select to send location UUID:path.
MCPServer sets currentPath in watchedDirectories

When starting a chain from a watched directory, ensure a SIP's
current path matches the one found in the directory.  This can happen
during AIP reingest, where the last know location is not the watched
directory it is currently in. Do not change currentPath for DIPs, as
they can run in parallel with the originating SIP and overwrite the
SIP's information.
ArchivematicaMCP: Cleanup

Dedupe and alphabetically sort imports. Move config fetching outside a
loop. Remove commented out code.
Transfer JS: Enable paths that don't start with /

refs #7133

Duracloud 'paths' may not start with /. Update JS to not insert /'s at the
start of every path.
Config fixes for Ubuntu 14.04

refs #7293

Apache now expects sites-[available|enabled] to end in .conf, so update dev
creation to create 000-default.conf

Gearman no longer creates a PID file that can be checked for. Instead,
check for the existance of the gearman process directly.
Dev-install: Do not install AtoM 1.3
Upstart: Add timeout waiting for Gearman
Dev-helper: Delete uploaded and stored DIPs

When clearing storage, also clear DIPs from storage.
connect_and_remove_transfer_files: delete full transfer from ES

Previously, this function queried the database for a list of files in
the transfer, and removed those specifically. However, since the
search index contains many files that aren't in the database (such
as logs and metadata files), this left dangling files that could
never be removed.

Instead query the database for transfers, then delete all files in ES
from each of those transfers.

refs #7357
use generic version of elasticSearch remove files method

refs #7357

When deleting files from the ElasticSearch index, take
advantage of the change in commit c0eb597c630a482ffcb8b2056b04f3f605265114
that provides a more generic remove method.
updating Archivematica version number in Agents table

in preparation for 1.3.0 release
Updating version number

in preparation for 1.3.0 release
characterizeFile: validate XML before inserting to DB

This ensures that if the characterization tool returns invalid XML,
it will not be saved to the database in order to avoid later issues
with createMETS2.

For instance, in some circumstances FITS may print error output to the
stdout stream alongside actual XML content, resulting in a document
that will not parse.

Fixes #7422.
characterizeFile: don't double-print stdout

stdout is already piped to the terminal as well as captured; the
print here would result in duplicated output.