Fix: some places still used the hard-coded connection timeouts that are now replaced by the configurable timeouts.

SVN: 28151

Add parameters remote-connection-timeout and remote-operation-timeout for setting timeouts of SSH remote connections and operations. This is to support slow hosts and networks (in particular Windows hosts using Cygwin binaries) that always timeout with the default settings.

SVN: 28144

Revert r27035 (rename ch.systemsx.cisd.common.exception back to ch.systemsx.cisd.common.exceptions) as it breaks backward compatibility of the public APIs.

SVN: 27469

SVN: 27144

SVN: 27143

Move timing-related constants from Constants to TimingParameters and move TimingParameters to sub-package time.

SVN: 27140

SVN: 27139

SVN: 27045

SVN: 27035

Move IDelegatedAction and ITerminable to package action, move ITimerTaskStatusProvier to package concurrent.

SVN: 27032

SVN: 27030

SVN: 27028

SVN: 27027

SVN: 27017

SVN: 27012

SVN: 27010

SVN: 27003

SVN: 26602

SVN: 26542

Make HostAwareFile and sub-classes internally use Strings for paths rather than java.io.Files to avoid any conversion being performed automatically by java.io.File.

SVN: 26513

SVN: 26113

SVN: 26106

SVN: 26105

SVN: 26091

SVN: 26079

SVN: 25954

SVN: 25538

SVN: 25498

SVN: 25462

SVN: 25296

SVN: 24125

SVN: 24107

SVN: 24041

GNU find (i.e findutils) command for at least version 4.4.2 spills out last modified timestamp in option -printf "%T@\n" with fractional parts. GNU find version 4.2.27 output are integer without fractional part. For that reason tryParseLastChangedMillis() parses the timestamp as a double value.

SVN: 23827

SVN: 23385

SVN: 22593

fix: on startup, check for each item of the .faulty_paths file whether it still exists and remove it, if it doesn't exist anymore

SVN: 21094

SVN: 21093

SVN: 21092

fix: if a file or directory could be copied successfully from incoming to buffer but subsequent deletion on incoming failed, datamover used to delete the correct copy in buffer; if the deletion of the file or directory on incoming was partially successful, this behavior lead to data loss as the only complete copy was deleted; now, on successful copying but failure on subsequent deletion, the path is added to .faulty_path and a NOTIFY log is done that an admin needs to remove the path manually, but the correct copy is not deleted but processing continues

SVN: 21091