Closes #2936

Previously, deprecation warnings were done as part of dependency lookups, which were run concurrently. This meant the chance of duplicate issues was high, due to race conditions. Instead, raising the issues is done once all package are looked up, to ensure only one issue per manager/dependency. It also means we can list all of the affected package files, in case of a monorepo.

Closes #2224, Closes #2225