storage: check uniqueness based on all relevant columns, not just id and indexer_configuration_id.

ctags and fossology can legitimately add multiple objects with the same
id and indexer_configuration_id at the same time, but different values
for other columns.

Before this commit, it would immediately crash the 'check_id_duplicates'
checks.

As a side-effect, this commit also remove the 'add_merge' logic in the
in-memory storage, and stores it like proper rows like the pg does instead
of working around this broken deduplication.

As an other side-effect, removing this broken logic removes an
inconsistency between the in-mem and pg storage (see the added tests
named test_add_empty for Ctags and Fossology), which Fossology indexer
tests relied on, so this commit updates these tests as well.