Making sure that tests in aa-prop run. They weren't running at all

Removing deprecated classes for biojava 4 release

The CLIs for most structure alignment algorithms derive from
AbstractUserArgumentParser, but there wasn't a good mechanism to
introduce new arguments, since all parameters are stored into a
bean.

Without refactoring everything, this makes the parameter specification
a bit more consistent. The standard parameters are still stored in
a StartupParameters bean, but this is extended by each class to store
the class-specific parameters. Help strings are taken from a
ConfigStrucAligParams subclass, which was previously only used for the
GUI parameters. So the GUI and CLI parameter lists should now match.

The procedure for adding a new CLI implementation is documented in
AbstractUserArgumentParser.

Methods converted to the new system:
* Ce
* CeCP
* FatCat
* SmithWaterman3D

Other AbstractUserArgumentParser implementations downstream of BioJava
will need to be updated to work with the new system.

printHelp() is now required for all UserArgumentProcessors
(moved from it's previous location in StructureAlignment.)
This allows -h, -help, and -version to be handled consistently
in the argument parser rather than in each aligner.

Also cleaned up some 'throw Exception/catch Exception' uses.

Finally, slightly changed the behavior of boolean arguments. Valid
values are nothing (determine value based on '-no' prefix), t/true,
and f/false. Other options give errors rather than defaulting to
false (the Boolean.parseBoolean() behavior).

Improvements to Structure alignment CLIs

- Don't print CE when -show3d is given

…r interface and is able to use the new GenbankSequenceParser

Adds accelerators (shortcuts, e.g. Ctrl-Q) for major menu items.
Redefine mnemonics (e.g. Alt-F Q) to remove redundant mnemonics

-added 2 test cases to GenbankReaderTest

reason there is an increment added in GenericInsdcHeaderFormat which is
responsible for this effect. Changing the increment to 0 patches the
writer.

… not make sense at this stage.

GenbankReader patch for multiple sequences from single file

This changes the behaviour of Compound.getChainIDs() to only return the
unique chain ids

The new resources already existed but they were not referenced to, now
also removed the old org/biojava/bio resource files too

before it was first model only.

The bug must have been introduced in 4.0 because Structure.clone() now
does full cloning of all models and I suppose before it wasn't.
Introduced test for quat symmetry detection.

and throwing exception. Related to #111