Clean install of 4.0.e fails on missing DB table?

[krtbuni]

TLDR version: Clean install of 4.0.e fails; error in catalina.out is "Table 'alfresco.alf_prop_class' doesn't exist"

Longer version:
Linux uname -a:  3.2.0-24-generic #39-Ubuntu SMP Mon May 21 16:52:17 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
DB: mysql  Ver 14.14 Distrib 5.5.24, for debian-linux-gnu (x86_64) using readline 6.2

Issues with installation scripts:
1) No option during installation to provide existing database connectivity.
2) No option during installation to provide existing webserver functionality.
3) No option during installation to specify existing FTP access.

Issues post-installation:

Database connection validated; schema updates worked fine, database tables created as expected. However, server refuses to start, throwing the indicated errors.

alfresco.xml:

<?xml version="1.0" encoding="UTF-8"?>
<Context>
  <!– Uncomment in $CATALINA_BASE/conf/[enginename]/[hostname]/alfresco.xml to define your own datasource. Add value attributes to each of the environment tags below to define your environment settings. –>
  <!– Resource defaultTransactionIsolation="-1" defaultAutoCommit="false" maxActive="100" initialSize="10" password="alfresco" username="alfresco" url="jdbc:mysql:///alfresco" driverClassName="org.gjt.mm.mysql.Driver" type="javax.sql.DataSource" auth="Container" name="jdbc/dataSource"/–>
  <Environment override="false" type="java.lang.Boolean" name="properties/startup.enable" description="A flag that globally enables or disables startup of the major Alfresco subsystems." value="true"/>
  <Environment override="false" type="java.lang.String" name="properties/dir.root" description="The filesystem directory below which content and index data is stored. Should be on a shared disk if this is a clustered installation." value="/opt/alfresco-4.0.e/data"/>
  <Environment override="false" type="java.lang.String" name="properties/hibernate.dialect" description="The fully qualified name of a org.hibernate.dialect.Dialect subclass that allows Hibernate to generate SQL optimized for a particular relational database. Choose from org.hibernate.dialect.DerbyDialect, org.hibernate.dialect.MySQLInnoDBDialect, org.alfresco.repo.domain.hibernate.dialect.AlfrescoOracle9Dialect, org.alfresco.repo.domain.hibernate.dialect.AlfrescoSybaseAnywhereDialect, org.alfresco.repo.domain.hibernate.dialect.AlfrescoSQLServerDialect, org.hibernate.dialect.PostgreSQLDialect" value="org.hibernate.dialect.MySQLInnoDBDialect"/>
  <Environment override="false" type="java.lang.String" name="properties/hibernate.query.substitutions" description="Mapping from tokens in Hibernate queries to SQL tokens. For PostgreSQL, set this to &quot;true TRUE, false FALSE&quot;." value=""/>
  <Environment override="false" type="java.lang.Boolean" name="properties/hibernate.jdbc.use_get_generated_keys" description="Enable use of JDBC3 PreparedStatement.getGeneratedKeys() to retrieve natively generated keys after insert. Requires JDBC3+ driver. Set to false if your driver has problems with the Hibernate identifier generators. By default, tries to determine the driver capabilities using connection metadata." value="false"/>
  <Environment override="false" type="java.lang.String" name="properties/hibernate.default_schema" description="Qualify unqualified table names with the given schema/tablespace in generated SQL. It may be necessary to set this when the target database has more than one schema." value="alfresco"/>
</Context>
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alfresco-global.properties (user/pass munged for security):

###############################
## Common Alfresco Properties #
###############################

dir.root=/opt/alfresco-4.0.e/alf_data

alfresco.context=alfresco
alfresco.host=127.0.0.1
alfresco.port=8080
alfresco.protocol=http

share.context=share
share.host=127.0.0.1
share.port=8080
share.protocol=http

### database connection properties ###
db.driver=org.gjt.mm.mysql.Driver
db.username=alfresco
db.password=XXX
db.name=XXX
db.url=jdbc:mysql://localhost:3306/alfresco?useUnicode=yes&characterEncoding=UTF-8

### FTP Server Configuration ###
ftp.enabled=true
ftp.port=8021
ftp.ipv6.enabled=false

### RMI service ports ###
alfresco.rmi.services.port=50500
avm.rmi.service.port=0
avmsync.rmi.service.port=0
attribute.rmi.service.port=0
authentication.rmi.service.port=0
repo.rmi.service.port=0
action.rmi.service.port=0
deployment.rmi.service.port=0

### External executable locations ###
ooo.exe=/opt/alfresco-4.0.e/openoffice/program/soffice.bin
ooo.enabled=true
ooo.port=8100
ooo.port=8100
img.root=/opt/alfresco-4.0.e/common
img.dyn=${img.root}/lib
img.exe=${img.root}/bin/convert
swf.exe=/opt/alfresco-4.0.e/common/bin/pdf2swf
jodconverter.enabled=false
jodconverter.officeHome=/opt/alfresco-4.0.e/openoffice
jodconverter.portNumbers=8100

### Initial admin password ###
alfresco_user_store.adminpassword=43c12db9cc44a72aba18c9c02fff075d

### E-mail site invitation setting ###
notification.email.siteinvite=false

### File Protocol Root ###
protocols.rootPath=/${spaces.company_home.childname}/${spaces.sites.childname}

### License location ###
dir.license.external=/opt/alfresco-4.0.e

### Solr indexing ###
index.subsystem.name=solr
dir.keystore=${dir.root}/keystore
solr.port.ssl=8443

### BPM Engine ###
system.workflow.engine.jbpm.enabled=false
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catalina.out:

2012-10-05 00:53:38,164  INFO  [management.subsystems.ChildApplicationContextFactory] [main] Starting 'sysAdmin' subsystem, ID: [sysAdmin, default]
 2012-10-05 00:53:38,328  INFO  [management.subsystems.ChildApplicationContextFactory] [main] Startup of 'sysAdmin' subsystem, ID: [sysAdmin, default] complete
 2012-10-05 00:53:51,892  WARN  [alfresco.util.AbstractTriggerBean] [main] Job ehCacheTracerJob is not active/enabled
 2012-10-05 00:53:58,719  INFO  [extensions.webscripts.TemplateProcessorRegistry] [main] Registered template processor Repository Template Processor for extension ftl
 2012-10-05 00:53:58,724  INFO  [extensions.webscripts.ScriptProcessorRegistry] [main] Registered script processor Repository Script Processor for extension js
 2012-10-05 00:54:12,216  INFO  [domain.schema.SchemaBootstrap] [main] Schema managed by database dialect org.hibernate.dialect.MySQLInnoDBDialect.
 2012-10-05 00:54:13,182  INFO  [domain.schema.SchemaBootstrap] [main] No changes were made to the schema.
 2012-10-05 00:54:47,919  ERROR [web.context.ContextLoader] [main] Context initialization failed
 org.alfresco.error.AlfrescoRuntimeException: 09050039 Keystores are invalid
        at org.alfresco.encryption.EncryptionChecker$1.execute(EncryptionChecker.java:71)
        at org.alfresco.encryption.EncryptionChecker$1.execute(EncryptionChecker.java:61)
        at org.alfresco.repo.transaction.RetryingTransactionHelper.doInTransaction(RetryingTransactionHelper.java:388)
        at org.alfresco.repo.transaction.RetryingTransactionHelper.doInTransaction(RetryingTransactionHelper.java:259)
        at org.alfresco.encryption.EncryptionChecker.onBootstrap(EncryptionChecker.java:60)
        at org.springframework.extensions.surf.util.AbstractLifecycleBean.onApplicationEvent(AbstractLifecycleBean.java:56)
        at org.alfresco.repo.management.SafeApplicationEventMulticaster.multicastEventInternal(SafeApplicationEventMulticaster.java:209)
        at org.alfresco.repo.management.SafeApplicationEventMulticaster.multicastEvent(SafeApplicationEventMulticaster.java:180)
        at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:303)
        at org.springframework.context.support.AbstractApplicationContext.finishRefresh(AbstractApplicationContext.java:911)
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:428)
        at org.springframework.web.context.ContextLoader.createWebApplicationContext(ContextLoader.java:276)
        at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:197)
        at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
        at org.alfresco.web.app.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:63)
        at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4135)
        at org.apache.catalina.core.StandardContext.start(StandardContext.java:4630)
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:791)
        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:771)
        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:546)
        at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:637)
        at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:563)
        at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:498)
        at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1277)
        at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:321)
        at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
        at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
        at org.apache.catalina.core.StandardHost.start(StandardHost.java:785)
        at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
        at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:445)
        at org.apache.catalina.core.StandardService.start(StandardService.java:519)
        at org.apache.catalina.core.StandardServer.start(StandardServer.java:710)
        at org.apache.catalina.startup.Catalina.start(Catalina.java:581)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:601)
        at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
Caused by: org.springframework.jdbc.BadSqlGrammarException:
### Error querying database.  Cause: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'alfresco.alf_prop_class' doesn't exist
### The error may involve alfresco.propval.select_PropertyClassByName-Inline
### The error occurred while setting parameters
### Cause: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'alfresco.alf_prop_class' doesn't exist
; bad SQL grammar []; nested exception is com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'alfresco.alf_prop_class' doesn't exist
        at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.doTranslate(SQLErrorCodeSQLExceptionTranslator.java:233)
        at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:72)
        at org.mybatis.spring.MyBatisExceptionTranslator.translateExceptionIfPossible(MyBatisExceptionTranslator.java:71)
        at org.mybatis.spring.SqlSessionTemplate$SqlSessionInterceptor.invoke(SqlSessionTemplate.java:346)
        at $Proxy6.selectOne(Unknown Source)
        at org.mybatis.spring.SqlSessionTemplate.selectOne(SqlSessionTemplate.java:154)
        at org.alfresco.repo.domain.propval.ibatis.PropertyValueDAOImpl.findClassByValue(PropertyValueDAOImpl.java:128)
        at org.alfresco.repo.domain.propval.AbstractPropertyValueDAOImpl$PropertyClassCallbackDAO.findByValue(AbstractPropertyValueDAOImpl.java:332)
        at org.alfresco.repo.domain.propval.AbstractPropertyValueDAOImpl$PropertyClassCallbackDAO.findByValue(AbstractPropertyValueDAOImpl.java:299)
        at org.alfresco.repo.cache.lookup.EntityLookupCache.getByValue(EntityLookupCache.java:364)
        at org.alfresco.repo.domain.propval.AbstractPropertyValueDAOImpl.getPropertyClass(AbstractPropertyValueDAOImpl.java:282)
        at org.alfresco.repo.domain.propval.ibatis.PropertyValueDAOImpl.findPropertyValueByValue(PropertyValueDAOImpl.java:336)
        at org.alfresco.repo.domain.propval.AbstractPropertyValueDAOImpl$PropertyValueCallbackDAO.findByValue(AbstractPropertyValueDAOImpl.java:775)
        at org.alfresco.repo.domain.propval.AbstractPropertyValueDAOImpl$PropertyValueCallbackDAO.findByValue(AbstractPropertyValueDAOImpl.java:712)
        at org.alfresco.repo.cache.lookup.EntityLookupCache.getByValue(EntityLookupCache.java:396)
        at org.alfresco.repo.domain.propval.AbstractPropertyValueDAOImpl.getPropertyValue(AbstractPropertyValueDAOImpl.java:699)
        at org.alfresco.repo.domain.propval.AbstractPropertyValueDAOImpl.deletePropertyUniqueContext(AbstractPropertyValueDAOImpl.java:1265)
        at org.alfresco.repo.attributes.AttributeServiceImpl.removeAttribute(AttributeServiceImpl.java:259)
        at org.alfresco.encryption.EncryptionKeysRegistryImpl.isKeyRegistered(EncryptionKeysRegistryImpl.java:133)
        at org.alfresco.encryption.AlfrescoKeyStoreImpl.validateKeys(AlfrescoKeyStoreImpl.java:880)
        at org.alfresco.encryption.AlfrescoKeyStoreImpl.validateKeys(AlfrescoKeyStoreImpl.java:187)
        at org.alfresco.encryption.KeyStoreChecker.validateKeyStores(KeyStoreChecker.java:47)
        at org.alfresco.encryption.EncryptionChecker$1.execute(EncryptionChecker.java:66)
        … 38 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'alfresco.alf_prop_class' doesn't exist
        at sun.reflect.GeneratedConstructorAccessor151.newInstance(Unknown Source)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:525)
        at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
        at com.mysql.jdbc.Util.getInstance(Util.java:386)
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1053)
        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4096)
        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4028)
        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2490)
        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2651)
        at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2734)
        at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2155)
        at com.mysql.jdbc.PreparedStatement.execute(PreparedStatement.java:1379)
        at org.apache.commons.dbcp.DelegatingPreparedStatement.execute(DelegatingPreparedStatement.java:172)
        at org.apache.commons.dbcp.DelegatingPreparedStatement.execute(DelegatingPreparedStatement.java:172)
        at org.apache.commons.dbcp.DelegatingPreparedStatement.execute(DelegatingPreparedStatement.java:172)
        at org.apache.ibatis.executor.statement.PreparedStatementHandler.query(PreparedStatementHandler.java:39)
        at org.apache.ibatis.executor.statement.RoutingStatementHandler.query(RoutingStatementHandler.java:55)
        at org.apache.ibatis.executor.SimpleExecutor.doQuery(SimpleExecutor.java:41)
        at org.apache.ibatis.executor.BaseExecutor.query(BaseExecutor.java:120)
        at org.apache.ibatis.executor.CchingExecutor.query(CachingExecutor.java:75)
        at org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:75)
        at org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:69)
        at org.apache.ibatis.session.defaults.DefaultSqlSession.selectOne(DefaultSqlSession.java:40)
        at sun.reflect.GeneratedMethodAccessor181.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:601)
        at org.mybatis.spring.SqlSessionTemplate$SqlSessionInterceptor.invoke(SqlSessionTemplate.java:338)
        … 57 more
Oct 05, 2012 12:54:52 AM org.apache.catalina.core.StandardContext start
SEVERE: Error listenerStart
Oct 05, 2012 12:54:52 AM org.apache.catalina.core.StandardContext start
SEVERE: Context [/alfresco] startup failed due to previous errors
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This is a clean, out-of-the-box install. Why can it not find its own database tables?

[krtbuni]

It's worth noting that installing as "Easy" instead of "Normal" worked as documented, but now I have two databases and two webservers running on the same box, which is less than optimal.