Bycon

This version provides a larger update to the multi-variant query concept. We now
provide:

* a proper version for using combined `variantQueryDigests`:
- [/beacon/datasets/progenetix/biosamples?filters=NCIT:C3058&variantQueryDigests=9:21500001-21975098--21967753-24000000:DEL,17:6000000-7687480--7668422-8000000:DEL](http://progenetix.test/beacon/datasets/progenetix/biosamples?filters=NCIT:C3058&variant_query_digests=9:21500001-21975098--21967753-24000000:DEL,17:6000000-7687480--7668422-8000000:DEL)
will e.g. process 2 bracket requests (for small CDKN2A and TP53 deletions)
and intersect the samples having both these changes; the same call works,
obviously, also for services: [/services/sampleplots?datasetIds=progenetix&filters=NCIT:C3058&variant_query_digests=9:21500001-21975098--21967753-24000000:DEL,17:6000000-7687480--7668422-8000000:DEL](http://progenetix.test/services/sampleplots?datasetIds=progenetix&filters=NCIT:C3058&variant_query_digests=9:21500001-21975098--21967753-24000000:DEL,17:6000000-7687480--7668422-8000000:DEL)
* a new (probably to be renamed `variantMultiPars` parameter which only works for
POST requests; _i.e._ each list entry has to be a proper variant query

"query": {
"requestParameters": {
"variantMultiPars": [
{
"assemblyId": "GRCh38",
"referenceName": "refseq:NC_000009.12",
"start": [21500001, 21975098],
"end": [21967753, 22500000],
"variantType": "DEL"
},
{
"assemblyId": "GRCh38",
"referenceName": "refseq:NC_000017.11",
"start": [6000000, 7687480],
"end": [7668422, 8000000],
"variantType": "DEL"
}
]
},
"filters": [{"id": "NCIT:C3058"}]
}


Also `bycon` now supports the default `/beacon/datasets/{id}/g_variants` etc. access
pattern for single dataset data retrieval (the use of the `datasetIds` parameter is
still not fully standard supported though it had been documented in the framework
... see [Github issue 123](https://github.com/ga4gh-beacon/beacon-v2/issues/123#issuecomment-2059711886)).

Multi-variant matches first pass

We now implement an experimental version of multi-variant matching, to retrieve
samples which show co-occurrence of 2 or more variants. This so far is limited to
a few parameters:

* NEW: `variantQueryDigests` in the form of `9:9000001-21975098--21967753-24000000:DEL`
- several of those can be comma-concatenated
- probably not final name or format
- only bracket matches & ranges working (but will change ...)
- different variant types can be used
* `geneId` has been morphed to a list parameter (though keeping the standard name)
- usual comma-concatenation etc.
- here only a global `variantType` can be provided
* future versions to implement mixed matches etc. (e.g. sequence variant & CNV)

Other ...

* fixed paginated handovers missing the `info.content_id` parameter which is used
by the progenetix-web etc. front ends
* changed the `cytoBands` argument to `type: array`, to allow definition of multiple
cytogenetic regions, e.g. to indicate fusions or bracket requests
- this might be a temporary solution for testing purposes and e.g. replaced
by a future parsing of simple statements like `t(8;14)(q24;q32)`
* moved some cytoband functionality to the main `bycon` package, from `byconaut`,
to allow processing of cytoband requests in the main Beacon service
* `byconaut` was restructured for exacutables, with `housekeepers` and `importers`
directories

* added `scopes` to `beacon/filtering_terms/`
- see <https://github.com/ga4gh-beacon/beacon-v2/pull/118>
* fixed bug where the default splitting of input parameters by comma led to over-splitting
of the "embedded list" values in `plotPars` (e.g. using `plotPars=plotGeneSymbols=MYC,T,TP53`
would lead to `plotPars=plotGeneSymbols=MYC::T::TP53` ... and later errors)
- now "non-list" strings w/ internal `,` are just re-joined & a warning is created

* configuration changes:
- `beacon_defaults` file changed to `entity_defaults` since only entities
defined in it
- paths are now defined within the entity definitions, no separate aliases etc.
- local overrides for the Beacon entity defaults now in `local/instance_definitions.yaml`
- for byconaut a separate `services_entity_defaults` file provides the additional
services (e.g. `sampleplots` ... pseudo-entities)

* adding a `__collections_response_remap_cohorts(self, colls=[])` function
to reformat the collections response for cohorts from the collations format
- TODO: define cohorts as separate entities which are read in during collations
generation, with their additional parameters etc.
* fixed the openAPI endpoints for collation responses (datasets & cohorts); are
[incorrect in current Beacon spec.](https://github.com/ga4gh-beacon/beacon-v2/issues/116)
* bug fix `byconaut`: matrix export was broken since 1.6.1
* exception capture for wrong form values: string values of "None", "none", "Null",
"null" from GET requests are now converted to logical `None` (i.e. removed)

* bug fix: individuals & phenopackets endpoints were broken in 1.6.0 due to missed
clean up in query code
* bug fix `byconaut`: vcf & pgsxseg exports were broken in 1.6.0 due to incomplete
clean-up of internal variant mapping
* bug fix `byconaut`: `/geolocations` queries were broken due to needed setting of
authorization / granularity, which was handled by `run_beacon_init_stack` which
however wasn't used by this service
* global change: removal of `run_beacon_init_stack` and inclusion of its
function calls in the ubiquitous `initialize_bycon_service`