Buildbot fixes and cleanups:

- Added --verbose to BUILD scripts to get make to write out compile commands.
- Detect if AM_EXTRA_MAKEFLAGS=VERBOSE=1 was used with build scripts.
- Don't write warnings about replication variables when doing bootstrap.
- Fixed that mysql_cond_wait() and mysql_cond_timedwait() will report original source file in case of errors.
- Ignore some compiler warnings

BUILD/FINISH.sh:
  Detect if AM_EXTRA_MAKEFLAGS=VERBOSE=1 or --verbose was used
BUILD/SETUP.sh:
  Added --verbose to print out the full compile lines
  Updated help message
client/mysqltest.cc:
  Fixed that one can use 'replace' with cat_file
cmake/configure.pl:
  If --verbose is used, get make to write out compile commands
debian/dist/Debian/rules:
  Added $AM_EXTRA_MAKEFLAGS to get VERBOSE=1 on buildbot builds
debian/dist/Ubuntu/rules:
  Added $AM_EXTRA_MAKEFLAGS to get VERBOSE=1 on buildbot builds
include/my_pthread.h:
  Made set_timespec_time_nsec() more portable.
include/mysql/psi/mysql_thread.h:
  Fixed that mysql_cond_wait() and mysql_cond_timedwait() will report original source file in case of errors.
mysql-test/suite/innodb/r/auto_increment_dup.result:
  Fixed wrong DBUG_SYNC
mysql-test/suite/innodb/t/auto_increment_dup.test:
  Fixed wrong DBUG_SYNC
mysql-test/suite/perfschema/include/upgrade_check.inc:
  Make test more portable for changes in *.sql files
mysql-test/suite/perfschema/r/pfs_upgrade.result:
  Updated test results
mysql-test/valgrind.supp:
  Ignore running Aria checkpoint thread
scripts/mysqlaccess.sh:
  Changed reference of bugs database
  Ensure that also client-server group is read.
sql/handler.cc:
  Added missing syncpoint
sql/mysqld.cc:
  Don't write warnings about replication variables when doing bootstrap
sql/mysqld.h:
  Don't write warnings about replication variables when doing bootstrap
sql/rpl_rli.cc:
  Don't write warnings about replication variables when doing bootstrap
sql/sql_insert.cc:
  Don't mask SERVER_SHUTDOWN in insert_delayed
  This is done to be able to distingush between shutdown and interrupt errors
support-files/compiler_warnings.supp:
  Ignore some compiler warnings in xtradb,innobase, oqgraph, yassl, string3.h

scripts/mysqlaccess.sh

@@ -930,7 +930,7 @@ sub MergeConfigFile {
                              $unsafeConfig = $fname;
                          }
                      }
-                     if ( $group eq 'client' ) {
+                     if ( $group eq 'client' || $group eq "client-server") {
                          $MYSQL_CNF{'mysql'}{$item} = $value;
                          $MYSQL_CNF{'mysqldump'}{$item} = $value;
                      } else {
@@ -2423,7 +2423,7 @@ sub Print_Header {
 sub Print_Footer {
     if ($MySQLaccess::CMD) { #command-line mode
     print "\n"
-         ."BUGs can be reported by email to bugs\@mysql.com\n";
+         ."BUGs can be reported trough https://mariadb.atlassian.net/browse/MDEV\n";
     }
     if ($MySQLaccess::CGI) { #CGI-BIN mode
     if ($MySQLaccess::Param{'brief'}) {
@@ -2431,7 +2431,7 @@ sub Print_Footer {
     }
     print "<HR>\n"
          ."<ADDRESS>\n"
-         ."BUGs can be reported by email to <a href=mailto:bugs\@mysql.com>bugs\@mysql.com</a><BR>\n"
+         ."BUGs can be reported through <a href=\"https://mariadb.atlassian.net/browse/MDEV\">MariaDB JIRA</a><BR>\n"
 #         ."Don't forget to mention the version $VERSION!<BR>\n"
          ."</ADDRESS>\n"
          ."</BODY>\n"