[ENSCORESW-2595] Implement a dodge to avoid Travis-specific perl segfault around disconnect_if_idle(); At present the issue only appears in gene.t and we may presume it isn't affecting real use.

Updates to add align_type column to dna_align_feature and protein_align_feature tables to support multiple align types and remove external_data column from dna_align_feature table - ENSCORESW-1937

Set an object's default version to 1 when it is created, rather than when it is stored, to allow undef versions (which can then be stored as NULLs in the database).

Done in response to PR #151 to expand on the tests running. Also cleaned
up a report's english.

This reverts commit 3e24194c.

stable_id_version setter/getter for core object types, sets stable_id with a . delimited version or fetches stable_id with .version concatonated (if version is set)

- Ensire the "version" if tested for is digits only

- Added support in the Registry for version ids (\.\d+) support in stable_id when determining idenfitier type
- Added support to the ArchiveStableIdAdaptor for versions in stable_ids on object creation
- Test cases for identifiers with and without versions when doing lookups

- handlers in Exon, Gene, Operon, OperonTranscript and Transcript Adaptors for a versions fetch_by_stable_id call and new handler for fetch_by_stable_id_version
- Translation is handled implicitly through calls to Transcript
- Test cases for the new handlers and functionality

Method runs a query across the ontology_xref table to find anything linked to a gene with a particular linkage type e.g. IMP or IDA. This brings back a set of IDs to then query for a gene by.

The subroutine fetch_all_by_Slice_and_external_dbname_link() seemed to
delegate to the SUPER::fetch_by_Slice_constraint() rather than using the
Slice based fetch method below it. Without using that method this did
not pay attention to the $load_transcripts flag.

A test case has also been written to use the method and make sure it
works.

This reverts commit 720ff4750e90aec9febc6c4bab3a41e133d0b314.

This reverts commit 856a5aa2.

not available with default installation
will come back under another form

Due to changes in BaseFeatureAdaptor we need to save the state of
meta_coord otherwise a number of tests will begin to fail. Same is
true of xref.