refactor(core): consolidate references

[thdxr]

Summary

• consolidate references into one Location-scoped core registry with normalized sources and internal Git materialization
• move config-backed reference registration into a config plugin and expose references through GET /api/reference
• remove legacy reference services, prompt metadata, and reference-aware tool inputs
• synchronize reference updates through EventV2 and the TUI SyncV2 store

Stack

• based on refactor(tui): centralize application exit #31524

Verification

• 68 focused core tests
• 60 focused opencode tests
• 8 SyncV2 tests
• core, server, opencode, and TUI typechecks
• repository pre-push typecheck: 23 tasks passed
• git diff --check

[greptile-apps]

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