Add recursive directory scanning to discover SKILL.md files in nested
directories. When a SKILL.md is found, treat sibling directories as
functional folders rather than separate skills.
- Replace INSERT OR REPLACE with UPDATE for existing providers to avoid
triggering ON DELETE CASCADE on provider_endpoints table
- Fix endpoint merging logic to correctly mark database endpoints as
isCustom when they overlap with preset endpoints
The root cause was that INSERT OR REPLACE performs DELETE + INSERT under
the hood, which triggered the foreign key cascade and deleted all
associated endpoints from provider_endpoints table.