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

include/mysql/psi/mysql_thread.h

@@ -477,7 +477,7 @@ typedef struct st_mysql_cond mysql_cond_t;
   Instrumented cond_wait.
   @c mysql_cond_wait is a drop-in replacement for @c pthread_cond_wait.
 */
-#ifdef HAVE_PSI_INTERFACE
+#if defined(HAVE_PSI_INTERFACE) || defined(SAFE_MUTEX)
   #define mysql_cond_wait(C, M) \
     inline_mysql_cond_wait(C, M, __FILE__, __LINE__)
 #else
@@ -491,7 +491,7 @@ typedef struct st_mysql_cond mysql_cond_t;
   @c mysql_cond_timedwait is a drop-in replacement
   for @c pthread_cond_timedwait.
 */
-#ifdef HAVE_PSI_INTERFACE
+#if defined(HAVE_PSI_INTERFACE) || defined(SAFE_MUTEX)
   #define mysql_cond_timedwait(C, M, W) \
     inline_mysql_cond_timedwait(C, M, W, __FILE__, __LINE__)
 #else
@@ -963,7 +963,7 @@ static inline int inline_mysql_cond_destroy(
 static inline int inline_mysql_cond_wait(
   mysql_cond_t *that,
   mysql_mutex_t *mutex
-#ifdef HAVE_PSI_INTERFACE
+#if defined(HAVE_PSI_INTERFACE) || defined(SAFE_MUTEX)
   , const char *src_file, uint src_line
 #endif
   )
@@ -980,7 +980,11 @@ static inline int inline_mysql_cond_wait(
       PSI_server->start_cond_wait(locker, src_file, src_line);
   }
 #endif
+#ifdef SAFE_MUTEX
+  result= safe_cond_wait(&that->m_cond, &mutex->m_mutex, src_file, src_line);
+#else
   result= pthread_cond_wait(&that->m_cond, &mutex->m_mutex);
+#endif
 #ifdef HAVE_PSI_INTERFACE
   if (likely(locker != NULL))
     PSI_server->end_cond_wait(locker, result);
@@ -992,7 +996,7 @@ static inline int inline_mysql_cond_timedwait(
   mysql_cond_t *that,
   mysql_mutex_t *mutex,
   struct timespec *abstime
-#ifdef HAVE_PSI_INTERFACE
+#if defined(HAVE_PSI_INTERFACE) || defined(SAFE_MUTEX)
   , const char *src_file, uint src_line
 #endif
   )
@@ -1009,7 +1013,12 @@ static inline int inline_mysql_cond_timedwait(
       PSI_server->start_cond_wait(locker, src_file, src_line);
   }
 #endif
+#ifdef SAFE_MUTEX
+  result= safe_cond_timedwait(&that->m_cond, &mutex->m_mutex, abstime,
+                              src_file, src_line);
+#else
   result= pthread_cond_timedwait(&that->m_cond, &mutex->m_mutex, abstime);
+#endif
 #ifdef HAVE_PSI_INTERFACE
   if (likely(locker != NULL))
     PSI_server->end_cond_wait(locker, result);