Use the extensions system for data file validators and metadata readers

[Nicklas Nordborg]

Related to ticket #1592. A similar solution as implemented for external file support (#1582) should be used.

One difference is that the API promises that a single instance of a validator/metadata reader is shared if used in more than one place. This is mostly because an implementation that is both a validator+metadata reader shouldn't have to parse the file twice.

[Nicklas Nordborg]

(In [5623]) References #1598: Use the extensions system for data file validators and metadata readers

There are major changes in this function. To summarize:

• The metadata extraction has been merged with the validation. There are no longer need for separate implementations.
• All information about which classes to use have been removed from the DataFileType class. Instead, each extension need to check if it can be used in a given context (eg. check the platform of the item).
• The net.sf.basedb.core.filehandler package has been removed. Generic classes has been moved to net.sf.basedb.util.fileset (but with big changes in the actual classes). Affymetrix-related classes have been moved to net.sf.basedb.util.Affymetrix. The existing functionality can be found with some minor changes plus that we have additions to hook into the extensions system.
• The docbook documentation we have about this needs to be updated
• The update scripts need to remove the four columns in the DateFileTypes table and all filters, etc. referencing those columns from the gui context information.

[Nicklas Nordborg]

(In [5624]) References #1591: Upgrade script for BASE 2.17 --> 3.0

References #1598: Use the extensions system for data file validators and metadata readers

Update that removes the four columns from the DataFileTypes table and remove all references to the properties from the context settings.

[Nicklas Nordborg]

Seems to be working well with the Illumina package so I am closing this now.