i am installing Appian 7.3 with jboss EAP 6.1.0 Final server. i am wondering why

You can create the necessary directories under modules.

If use the Appian Configuration Manager (forum.appian.com/.../Appian_Configuration_Manager) all these folders and the setup will be completed by the Manager.

i am getting following error.
2013-12-17 17:49:01,018 [ServerService Thread Pool -- 65] ERROR org.hibernate.connection.DatasourceConnectionProvider - Could not find datasource: jdbc/MySqlDataSource1

APPIAN-DS :
<xa-datasource

jndi-name="jdbc/MySqlDataSource1"

pool-name="MySqlDS"

enabled="true"

use-java-context="false">

& entry to CUSTOM:PROPERTIES is like below
conf.data.primary.datasource=jdbc/MySqlDataSource

tried like below also , but dint get any luck..
java:/jdbc/MySqlDataSource

JNDI name needs to be the same as the name you define in custom.properties.

yes its same but still shows error

013-12-17 18:21:57,424 [ServerService Thread Pool -- 93] INFO com.appiancorp.rdbms.config.PrimaryDataSourceConfig - Validating and initializing the primary data source: java:/jdbc/MySqlDataSource
2013-12-17 18:21:57,990 [ServerService Thread Pool -- 93] ERROR org.hibernate.connection.DatasourceConnectionProvider - Could not find datasource: java:/jdbc/MySqlDataSource
javax.naming.NameNotFoundException: Error looking up jdbc/MySqlDataSource, service service jboss.naming.context.java.jdbc.MySqlDataSource is not started
          at org.jboss.as.naming.ServiceBasedNamingStore.lookup(ServiceBasedNamingStore.java:132)
          at org.jboss.as.naming.ServiceBasedNamingStore.lookup(ServiceBasedNamingStore.java:80)
          at org.jboss.as.naming.NamingContext.lookup(NamingContext.java:197)
          at org.jboss.as.naming.InitialContext.lookup(InitialContext.java:120)

1. Please stop Jboss.
2. Remove java:/ from your JNDI name in custom.properties since you have defined the java context as false in appian-ds.xml.
3. Restart Jboss.
Do you still see the same issues?

yes same issue...

2013-12-17 18:43:33,349 [ServerService Thread Pool -- 86] INFO com.appiancorp.rdbms.config.PrimaryDataSourceConfig - Validating and initializing the primary data source: jdbc/AppianPrimaryDS
2013-12-17 18:43:34,004 [ServerService Thread Pool -- 86] ERROR org.hibernate.connection.DatasourceConnectionProvider - Could not find datasource: jdbc/AppianPrimaryDS
javax.naming.NameNotFoundException: Error looking up jdbc/AppianPrimaryDS, service service jboss.naming.context.java.jdbc.AppianPrimaryDS is not started
          at org.jboss.as.naming.ServiceBasedNamingStore.lookup(ServiceBasedNamingStore.java:132)
          at org.jboss.as.naming.ServiceBasedNamingStore.lookup(ServiceBasedNamingStore.java:80)
          at org.jboss.as.naming.NamingContext.lookup(NamingContext.java:197)
          at org.jboss.as.naming.InitialContext.lookup(InitialContext.java:120)
          at org.jboss.as.naming.NamingContext.lookup(NamingContext.java:183)
          at org.jboss.as.naming.NamingContext.lookup(NamingContext.java:179)
          at javax.naming.InitialContext.lookup(InitialContext.java:411)
          at org.hibernate.connection.DatasourceConnectionProvider.configure(DatasourceConnectionProvider.java:75)
          at org.hibernate.connection.ConnectionProviderFactory.newConnectionProvider(ConnectionProviderFactory.java:143)
          at org.hibernate.ejb.InjectionSettingsFactory.createConnectionProvider(InjectionSettingsFactory.java:51)
          at org.hibernate.cfg.SettingsFactory.buildSettings(SettingsFactory.java:90)
          at org.hibernate.cfg.Configuration.buildSettingsInternal(Configuration.java:2836)
          at org.hibernate.cfg.Configuration.buildSettings(Configuration.java:2832)
          at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1843)
          at org.hibernate.ejb.Ejb3Configuration.buildEntityManagerFactory(Ejb3Configuration.java:906)
          at com.appiancorp.rdbms.hb.HbConfigurationHelper$1.call(HbConfigurationHelper.java:40)
          at com.appiancorp.rdbms.hb.HbConfigurationHelper$1.call(HbConfigurationHelper.java:37)
          at com.appiancorp.common.ContextClassLoaderSwitcher.runInContext(ContextClassLoaderSwitcher.java:21)
          at com.appiancorp.rdbms.hb.HbConfigurationHelper.buildEntityManagerFactory(HbConfigurationHelper.java:44)
          at com.appiancorp.rdbms.hb.DataSourceManagerHbImpl.getEntityManagerFactory(DataSourceManagerHbImpl.java:584)
          at com.appiancorp.rdbms.hb.DataSourceManagerHbImpl.getSessionFactory(DataSourceManagerHbImpl.java:577)
          at com.appiancorp.rdbms.hb.DataSourceManagerHbImpl.initialize(DataSourceManagerHbImpl.java:413)
          at com.appiancorp.rdbms.config.PrimaryDataSourceConfig.finish(PrimaryDataSourceConfig.java:22)
          at com.appiancorp.common.config.ConfigObject.init(ConfigObject.java:66)
          at com.appiancorp.common.config.ConfigObjectRepository.initConfigObject(ConfigObjectRepository.java:313)
          at com.appiancorp.common.config.ConfigObjectRepository.initConfigObject(ConfigObjectRepository.java:222)
          at com.appiancorp.common.config.ConfigObjectRepository.init(ConfigObjectRepository.java:181)
          at com.appiancorp.common.config.ConfigObjectRepository.create(ConfigObjectRepository.java:53)
          at com.appiancorp.common.config.ConfigObjectRepository.create(ConfigObjectRepository.java:47)
          at com.appiancorp.common.config.ConfigurationLoader.contextInitialized(ConfigurationLoader.java:39)
          at org.apache.catalina.core.StandardContext.contextListenerStart(StandardContext.java:3339)
          at org.apache.catalina.core.StandardContext.start(StandardContext.java:3777)
          at org.jboss.as.web.deployment.WebDeploymentService.doStart(WebDeploymentService.java:156)
          at org.jboss.as.web.deployment.WebDeploymentService.access$000(WebDeploymentService.java:60)
          at org.jboss.as.web.deployment.WebDeploymentService$1.run(WebDeploymentService.java:93)
          at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
          at java.util.concurrent.FutureTask.run(FutureTask.java:262)
          at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
          at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
          at java.lang.Thread

It looks like you keep changing your JNDI name as this error message shows the jdbc/AppianPrimaryDS.
Please try the following:
conf.data.primary.datasource=jdbc/appianPrimary
in custom.properties

<xa-datasource
jndi-name="jdbc/appianPrimary"
in appian-ds.xml