change: move file system related classes from ch.systemsx.cisd.common.utilities to ch.systemsx.cisd.common.filesystem

SVN: 7906

change: QueueingPathRemoverService to only offer static methods that are then used by FileOperations

SVN: 7904

SVN: 7902

SVN: 7901

SVN: 7885

SVN: 7884

SVN: 7883

SVN: 7882

SVN: 7866

SVN: 7864

SVN: 7863

SVN: 7862

remove: - Programmatic error from 'MigrationStepFrom022To23'.

SVN: 7861

- Simplify a bit 'JavaMigrationStepExecutor'.

SVN: 7858

change: make the setup of the tests more robust with regard to 'vanishing files' (since we have a QueueingPathRemover running)

SVN: 7856

[LMS-531] change: - 'database_instance_code' to 'database_instance' (same as experiment identifier).
- 'SampleWithOwner' should override 'equals' and 'hashCode' methods.
add: - 'instance_global_code'.

SVN: 7855

SVN: 7849

LMS-529 DatabaseAdminDAO extended by getDatabaseDefinition which returns DatabaseDefinition with meta data needed for merging databases.

SVN: 7845

SVN: 7844

- remove: commands help and version as they are not yet supported
- make it read a configuration file that can configure JAVA_HOME_, JAVA_OPTS and MAXLOGS
merged from branch 8.04.x

SVN: 7843

SVN: 7842

SVN: 7841

[LMS-472] Solve performance problem of BDS dataset creation and process triggering on trunk
merged from branch 8.04.x, improvements for 8.04.3

SVN: 7832

SVN: 7831

SVN: 7825

SVN: 7823

SVN: 7816

change: - Switch to BDS version 1.1 (v1.0 before).

SVN: 7815

change: - allow to specify crowd.server.host and crowd.server.port also in CIFEX and Datamover Console service.properties
- change CrowdAuthenticationService constructor such that it can cope with the port not being set in service.properties (int -> String)
- rename property crowd.server.url to crowd.server.host in service.property of lims)

SVN: 7813

Add useful assertion method to check that the message contains certain substring and return meaningful error message otherwise.

SVN: 7805

- implement performance improvements for slow remote file shares in class HCSImageFormattedData
[LMS-472] Solve performance problem of BDS dataset creation and process triggering on trunk
merged from branch 8.04.x, improvements for 8.04.3

SVN: 7802

- fine-grained activity in MonitoringProxy
- logging in ConcurrencyUtilities
- list*() methods to FileUtilities
[LMS-472] Solve performance problem of BDS dataset creation and process triggering on trunk
merged from branch 8.04.x, improvements for 8.04.3 common

SVN: 7800

change: improve CheckedExceptionTunnel: wrap IOException and ThreadDeath exception in their unchecked counter parts
[LMS-472] Solve performance problem of BDS dataset creation and process triggering on trunk
merged from branch 8.04.x, improvements for 8.04.3

SVN: 7797

add: classes ExtendedLinkedBlockingQueue, RecordBasedQueuePersister, PersistentExtendedBlockingQueueDecorator (needed for QueueingPathRemoverService)
[LMS-472] Solve performance problem of BDS dataset creation and process triggering on trunk
merged from branch 8.04.x, improvements for 8.04.3

SVN: 7796

SVN: 7795

SVN: 7786

SVN: 7782

SVN: 7764

SVN: 7710

SVN: 7678