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Why I can see some DB workload even when Syncope is idle?

This happens because Syncope delegates to Quartz the handling of scheduled jobs.

Jobs take care of reporting, notification, propagation, synchronization from external resources and also user-defined actions.

I get the error "WorkflowException: ... No outgoing sequence flow..." when updating an user

This means that the given user has a workflow state for which no update is allowed.
Such constraints are contained in the default worklfow XML definition that can be extended an customized through the administration console.

I get the error "An error occurred while registering a ClassTransformer with PersistenceUnitInfo..." during startup

This is harmless according to OpenJPA.

In embedded mode I get the error "Deployable http://localhost:9080/cargocpc/index.html failed to finish deploying within the timeout period 120000. The Deployable state is thus unknown"

This barely means that 2 minutes are not enough for setting up everything on the given hardware: you can configure this timeout by changing, in console/pom.xml:

      <plugin>
        <groupId>org.codehaus.cargo</groupId>
        <artifactId>cargo-maven2-plugin</artifactId>
        <inherited>true</inherited>
        <configuration>
          <container>

to

      <plugin>
        <groupId>org.codehaus.cargo</groupId>
        <artifactId>cargo-maven2-plugin</artifactId>
        <inherited>true</inherited>
        <configuration>
          <container>
            <timeout>180000</timeout>
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