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).

also some ergonomical changes:
- get a count+ is test replaced by is_count method
- variable names declared at the top of the modules, so can easily change gene/dbid/db used if the test database changes

Changed expected GTF in some cases: the start/stop codons should not have been there (incomplete CDS annotation)

Modified the enum on object_xref from 72->73 patch c and the redump
re-did some data. Such as choosing a different encoding for some very
small values. All changes are small though.

now fully testing patches and haplotypes

allows testing on patches and similar

using current_schema_no_cvs everywhere now

The big post-merge alt allele commit. Changes to alt_allele table, new tests, and a couple of new objects.

currently not compatible with most existing tests

An option from the command-line (-current-schema-no-cvs) allows to load the
schema from the file system instead of fetching it from the CVS repository.

was not tested by PAR, as patches are stored on scaffolds, ie a different coord system