added test for 'fetch_all_by_feature_class' with density features

Other schemas may need this which do not go through a process of removing
old/retired seq region ids in favour of their new ids. When querying by a slice
this is automatically delt with. When fetching by an ID you now need to
force the search on.

It seems that $DBI::errstr has a very strange life. We can get the error message
recived by incorrect connections or bad drivers (DBD::mysql is missing) when we
just warn the error. However concatenating it into another string makes the
message disapear. Even assignment and then concat will not work. Instead we
have switched to using the $@. This has the error in it.

replaced ok tests with is where possible
replaced core test database with patch database

We needed more methods to be able to handle alt allele group interactions. We also
needed to make sure a single gene could not be added more than once. Think we got
this one fixed

Removed dependencies on non-core APIs.

Added just a test for the new method filter_dir at the moment.

updated test cases to check integrity of api once deprecated tables, columns and methods have been removed
test databases patched to schema 74

Committing since we are now beyond the branch point in the API. This
allows a FullIdCache to key on various alternative identifiers/keys
generated by the implementing class. It means that if you want this
functionality you need to sub-class FullIdCache.

is not required for ontology database but allows for compatibility with metacontainer and schema version control like other databases

allows for future schema patching
added single table.sql file, replaces the need for individual sql files for each table

also updated existing tests to use is rather than ok whenever possible

The test schema was out of sync for ages due to it never being patched
using the patch sets. This is no longer the case. We needed a one
shot resynchronisation between the live schema and this test schema. All
test cases have been run and still pass. Assuming the processes
has not destroyed data. Any data changes seem to be related to different
levels of precision being emitted in the files.

Meta coord was updated.

patch was mentioned in meta table but not actually applied

when inserting 3 entries in parallel, should only store once
but depending on how fast mysql catches up, the return dbID corresponds to the first or the last attempt
now allowing for this change of mind

After talking to Compara we found the need to support additional
lookups with the full id cache. Since all values are stored in memory
the lookup is very easy to compute.

To provide improved querying of caches we now support SQL statements. These
queries return a list of keys (normally primary key db identifiers) defining
a list of objects to return. It is up to sub-BaseCache implementations to
deal with the nitty gritty of cache mis-hits (something they need to do
anyway).

Nathan requested methods which can perform this kind of task (assert the contents
of a data structure). We support 1 level of arrays and hashes. All test cases
pass at time of writing. Methods for capturing method returns were
not implemented. They do not fit into the Utils way of doing (no method
actually performs a task on an object they just report what it is).