remove: - 'register-controls', 'register-oligos' and 'register-viruses' commands.

SVN: 8078

SVN: 8015

SVN: 8005

SVN: 7979

change: - 'DataStructureV1_1' loads a 'ExperimentIdentifierWithUUID'.

SVN: 7977

change: - Global code renamed in UUID all over the code.

SVN: 7925

SVN: 7918

SVN: 7916

SVN: 7914

- 'performClosing' should be performed before the version is written out.

SVN: 7913

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

SVN: 7906

[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: 7831

SVN: 7823

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

SVN: 7815

- 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: include native libraries into datamover.jar

SVN: 7420

minor: - @Test class annotation on 'EqualsHashCodeTestCase' extensions.
change: - 'RoleWithCode' changed to 'RoleWithIdentifier' (code is not unique for group).
- 'PredicateStore' renamed to 'PredicateFactory' (Predicate instances no longer stored).

SVN: 7382

SVN: 7062

SVN: 7051

SVN: 7042

refactor: distinguish between copiers that perform immutable copies of files and copiers that perform immutable copies of directories (as a particular implementation may not be good for both)
add: methods for checking readable access to files or directories in FileUtilities

SVN: 7009

- better structure methods in RecursiveHardLinkMaker

SVN: 6978

SVN: 6791

[LMS-460] change r6673 such that the library writes out TRUE and FALSE but accepts all capitalizations when reading

SVN: 6774

SVN: 6684

SVN: 6683

SVN: 6682

SVN: 6681

SVN: 6679

change: - BDS does not write 'TRUE' but 'true' for flag parameters.

SVN: 6673

SVN: 6670

SVN: 6642

SVN: 6641

SVN: 6638

remove: - 'arg4j' library from 'libraries' project.

SVN: 6598

SVN: 6503

- Some test data for the BDS Structure Checker.
- Run configuration file to start the BDS Structure from Eclipse.

SVN: 6443