indexing stops working completely after intermittent connection issue

Steps to reproduce :

1. Install Confluence 5.8 with MySQL server
2. Login to Confluence
3. Shut down MySQL server
4. Open the atlassian-confluence.log with a text editor which can be found in <confluence_home_directory>/logs and take a look, you will see the following error :

   2015-11-27 16:19:20,002 ERROR [scheduler_Worker-3] [sf.hibernate.util.JDBCExceptionReporter] logExceptions Communications link failure
   
   The last packet successfully received from the server was 19,981 milliseconds ago.  The last packet sent successfully to the server was 0 milliseconds ago.
   2015-11-27 16:19:24,539 ERROR [scheduler_Worker-3] [org.quartz.core.ErrorLogger] schedulerError Unable to notify JobListener(s) of Job to be executed: (Job will NOT be executed!). trigger= DEFAULT.ConfluenceDavSessionInvalidatorJobDetail job= DEFAULT.ConfluenceDavSessionInvalidatorJobDetail
   org.quartz.SchedulerException: JobListener 'ScheduledJobListener' threw exception: Could not open Hibernate Session for transaction; nested exception is net.sf.hibernate.exception.GenericJDBCException: Cannot open connection [See nested exception: org.springframework.transaction.CannotCreateTransactionException: Could not open Hibernate Session for transaction; nested exception is net.sf.hibernate.exception.GenericJDBCException: Cannot open connection]
   	at org.quartz.core.QuartzScheduler.notifyJobListenersToBeExecuted(QuartzScheduler.java:1908)
   	at org.quartz.core.JobRunShell.notifyListenersBeginning(JobRunShell.java:335)
   	at org.quartz.core.JobRunShell.run(JobRunShell.java:173)
   	at com.atlassian.confluence.schedule.quartz.ConfluenceQuartzThreadPool$1.run(ConfluenceQuartzThreadPool.java:20)
   	at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:549)
   Caused by: org.springframework.transaction.CannotCreateTransactionException: Could not open Hibernate Session for transaction; nested exception is net.sf.hibernate.exception.GenericJDBCException: Cannot open connection
   	at org.springframework.orm.hibernate.HibernateTransactionManager.doBegin(HibernateTransactionManager.java:473)
   	at org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:374)
   	at org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:263)
   	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:101)
   	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
   	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
   	at com.sun.proxy.$Proxy99.jobToBeExecuted(Unknown Source)
   	at org.quartz.core.QuartzScheduler.notifyJobListenersToBeExecuted(QuartzScheduler.java:1906)
   	... 4 more
   Caused by: net.sf.hibernate.exception.GenericJDBCException: Cannot open connection
   	at net.sf.hibernate.exception.ErrorCodeConverter.handledNonSpecificException(ErrorCodeConverter.java:90)
   	at net.sf.hibernate.exception.ErrorCodeConverter.convert(ErrorCodeConverter.java:79)
   	at net.sf.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:29)
   	at net.sf.hibernate.impl.BatcherImpl.convert(BatcherImpl.java:328)
   	at net.sf.hibernate.impl.BatcherImpl.openConnection(BatcherImpl.java:295)
   	at net.sf.hibernate.impl.SessionImpl.connect(SessionImpl.java:3388)
   	at net.sf.hibernate.impl.SessionImpl.connection(SessionImpl.java:3348)
   	at org.springframework.orm.hibernate.HibernateTransactionManager.doBegin(HibernateTransactionManager.java:422)
   	... 11 more
   Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
   
   The last packet successfully received from the server was 19,981 milliseconds ago.  The last packet sent successfully to the server was 0 milliseconds ago.
   	at sun.reflect.GeneratedConstructorAccessor444.newInstance(Unknown Source)
   	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
   	at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
   	at com.mysql.jdbc.Util.handleNewInstance(Util.java:400)
   	at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1038)
   	at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3434)
   	at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3334)
   	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3774)
   	at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2447)
   	at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2594)
   	at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2541)
   	at com.mysql.jdbc.ConnectionImpl.setTransactionIsolation(ConnectionImpl.java:5167)
   	at com.mchange.v2.c3p0.impl.NewProxyConnection.setTransactionIsolation(NewProxyConnection.java:701)
   	at net.sf.hibernate.connection.C3P0ConnectionProvider.getConnection(C3P0ConnectionProvider.java:36)
   	at net.sf.hibernate.impl.BatcherImpl.openConnection(BatcherImpl.java:292)
   	... 14 more
   Caused by: java.net.SocketException: Software caused connection abort: recv failed
   	at java.net.SocketInputStream.socketRead0(Native Method)
   	at java.net.SocketInputStream.read(SocketInputStream.java:152)
   	at java.net.SocketInputStream.read(SocketInputStream.java:122)
   	at com.mysql.jdbc.util.ReadAheadInputStream.fill(ReadAheadInputStream.java:100)
   	at com.mysql.jdbc.util.ReadAheadInputStream.readFromUnderlyingStreamIfNecessary(ReadAheadInputStream.java:143)
   	at com.mysql.jdbc.util.ReadAheadInputStream.read(ReadAheadInputStream.java:173)
   	at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:2923)
   	at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3344)

5. Start MySQL database server again
6. Try and create a page named "testing unique result"
7. Type the string "testing unique result" in the search bar and you will see the following page with no result :
   

Expected result : The search should work as normal for subsequent creation of new pages after encountering intermittent connection issue. The index scheduler should continue executing as usual once Confluence is able to communicate with the MySQL database server. This expected behavior can be observed in Confluence 5.4 and 5.5 (have not tested other version yet)

Current result : the index scheduler completely stop working in Confluence unless it is being restarted and search is not workable for all newly created Space and Pages. This includes the "All Updates" tab not being updated in the Confluence dashboard.

Note : This issue affects Oracle and MS SQL server as well. It will potentially affects other database types as well. You can replicate this issue on a completely new Confluence instance.