PT-2140 - Update modules in the main branch (#570)

* PT-2140 - Update modules in the main branch

Updated modules for:
- pt-align
- pt-archiver
- pt-config-diff
- pt-deadlock-logger
- pt-diskstats
- pt-duplicate-key-checker
- pt-fifo-split
- pt-find
- pt-fingerprint
- pt-fk-error-logger
- pt-heartbeat
- pt-index-usage
- pt-ioprofile
- pt-kill
- pt-mext
- pt-mysql-summary
- pt-online-schema-change
- pt-pmp
- pt-query-digest
- pt-show-grants
- pt-sift
- pt-slave-delay
- pt-slave-find
- pt-slave-restart
- pt-summary
- pt-table-sync
- pt-upgrade
- pt-variable-advisor

Added execute bit for pt-query-digest

* PT-2140 Update modules in the main branch

Fixed Daemon.pm plugin usage
Updated all tests, related to the Daemon plugin.
I intentionally did not fix failing tests, not related to Daemon plugin,
to avoid making this PR too big.

- bin/pt-archiver
	- PT-2141 - Fixed usage of Daemon.pm
	- PT-2141 - Updated t/pt-archiver/standard_options.t
- bin/pt-deadlock-logger
	- PT-2143 - Fixed usage of Daemon.pm
	- PT-2143 - Updated t/pt-deadlock-logger/standard_options.t
- bin/pt-fifo-split
	- PT-2144 - Fixed usage of Daemon.pm
	- PT-2144 - Updated t/pt-fifo-split/pt-fifo-split.t
- bin/pt-find
	- PT-2145 - Fixed usage of Daemon.pm
	- PT-2145 - Updated t/pt-find/pt-find.t
- bin/pt-fk-error-logger
	- PT-2146 - Fixed usage of Daemon.pm
	- PT-2146 - Updated t/pt-fk-error-logger/basics.t
- bin/pt-heartbeat
	- PT-2147 - Fixed usage of Daemon.pm
	- PT-2147 - Updated t/pt-heartbeat/standard_options.t, t/pt-heartbeat/basics.t
- bin/pt-kill
	- PT-2148 - Fixed usage of Daemon.pm
	- PT-2148 - Updated t/pt-kill/standard_options.t
- bin/pt-show-grants
	- PT-2152 - Fixed usage of Daemon.pm
	- PT-2152 - Updated t/pt-show-grants/standard_options.t
- bin/pt-slave-delay
	- Fixed usage of Daemon.pm
	- Updated t/pt-slave-delay/standard_options.t
- bin/pt-slave-find
	- PT-2153 - Fixed usage of Daemon.pm
	- PT-2153 -Updated t/pt-slave-find/pt-slave-find.t
- bin/pt-slave-restart
	- Fixed usage of Daemon.pm
	- Updated t/pt-slave-restart/pt-slave-restart.t
- bin/pt-table-sync
	- PT-2154 - Fixed usage of Daemon.pm
	- PT-2154 -Updated t/pt-table-sync/standard_options.t

t/pt-deadlock-logger/standard_options.t

@@ -67,7 +67,7 @@ $output = output(
 
 like(
    $output,
-   qr{PID file $pid_file already exists},
+   qr{PID file $pid_file exists},
    'Dies if PID file already exists (--pid without --daemonize) (issue 391)'
 );
 
@@ -82,6 +82,8 @@ $sb->load_file('master', 't/pt-deadlock-logger/samples/deadlocks_tbl.sql', 'test
 
 $output = `$trunk/bin/pt-deadlock-logger $dsn --dest D=test,t=deadlocks --daemonize --run-time 10 --interval 1 --pid $pid_file 1>/dev/null 2>/dev/null`;
 
+#REMOVEME
+`echo "test 3" >>/tmp/REMOVEME`;
 PerconaTest::wait_for_files($pid_file);
 
 $output = `ps x | grep 'pt-deadlock-logger $dsn' | grep -v grep`;
@@ -91,6 +93,8 @@ like(
    'It lives daemonized'
 ) or diag($output);
 
+#REMOVEME
+`echo "test 4" >>/tmp/REMOVEME`;
 my ($pid) = $output =~ /(\d+)/;
 
 ok(
@@ -127,7 +131,7 @@ $output = output(
 
 like(
    $output,
-   qr/PID file $pid_file already exists/,
+   qr/PID file $pid_file exists/,
    'Does not run if PID file already exists'
 );