PackageManager::Base.save_dependencies: fix some major low-hanging performance fruit

[tiegz]

three changes to speed up PackageManager::Base.save_dependencies:

• across all versions, cache the lookup of dep platform/name to project_id, so we don't make repetitive calls to Project.find_best! for the same projects (since most versions are likely to have similar deps as other versions)
• for each version, extract a single list of existing dep names instead of iterating over the entire version.dependencies association for each dep
• for each version, aggregate all the deps into a single array, and insert them via insert_all instead of doing single inserts for each one

locally, these changes take a cold update of:

• npm/@docus/app from ~25sec to ~1.5sec.
• npm/gatsby from 83min to 67 sec