Improve error/warning message display when selecting plug-ins

[Nicklas Nordborg]

When selecing a plug-in the current list of warnings from other, seemingly unrelated plug-ins, are annoying. A typical message is: Unsupported raw data type: Agilent which comes from a plug-in configured for Genepix import. This message and other similar message, shouldn't be displayed. The problem is that there are other messages that may be important. For example if the JAR file for a plug-in is missing: JAR file not found: /usr/base/plugins/JarPlugin.jar

Support for two levels or errors/warnings must be added to the core and the web client must make use of it.

This ticket is also related to #376.

[Nicklas Nordborg]

(In [3438]) References #625. Added some infrastructure and moved context checking into the core.

[Nicklas Nordborg]

(In [3495]) References #625. Major features are now in place. It's a bit tricky to update the isInContext method on all plug-ins. I need more testing time to verify that all works before I close the ticket.

[Nicklas Nordborg]

(In [3519]) References #625. Fixed ClassCastException when using auto-detect and it found more than one matching file format

[Nicklas Nordborg]

There is a problem if only one out of several possible plug-ins can be used in a given context. See #657.

[Martin Svensson]

(In [3536]) References #625. This will correct the issue related to #657

[Nicklas Nordborg]

(In [3559]) References #625. Use correct plugin configuration.

[Nicklas Nordborg]

(In [3628]) References #625: PrintMapFlatFileImporter.isInContext now checks if the array design has plates connected to it.