Improving and unifying the setting of PDB_DIR and PDB_CACHE_DIR
- also improvements for #111 and #155
- some more work to do to make sure AtomCache and the Readers don't
double read the environment variables/system properties
More consolidation on PDB_DIR/PDB_CACHE_DIR reading
- reduced the number of initialisations in AtomCache and readers
- now all chem comp providers use PDB_CACHE_DIR
- a few #111 and #155 fixes
Redoing exception handling in test by using junit4's "expected" #111
SIFTS dir now also goes to PDB_CACHE_DIR instead of PDB_DIR
Cath files now also go to PDB_CACHE_DIR
Making tests use split dir layout
More fixes for PDB_DIR reading, plus some #111 and #155
Another small fix for PDB_DIR
Fixed several bugs, potentially calling with null argument, and having
array print contents of array instead of address
Fixed bug, class defines clone method but did not implement Cloneable
interface
Renaming CACHE_DIR to match its value (PDB_CACHE_DIR)

Also removed duplicate definitions
Removing duplicate PDB_DIR definitions.

Everything should use UserConfiguration.PDB_DIR
AtomImpl (serialized class) has member variable class Bond that is not
serialized. Bond class serialized.
Fixed bug, class that implemented clone method did not implement
Cloneable interface
Fixed bug, instance variable tranformationMap in serialized class
PDBHeader was not serializable
Merge pull request #186 from benjamintboyle/master

Bug fixes, in structure base package
Merge pull request #1 from sbliven/pdbdir

Renaming CACHE_DIR to match its value (PDB_CACHE_DIR)
Now PDB_DIR doesn't have to be writable
Merge pull request #180 from josemduarte/master

Consolidating PDB_DIR/PDB_CACHE_DIR reading
Implementing #181