Drop the isManual flag from ElementReference and the discovery-state methods
from RegistryInterface. The Registry becomes a flat last-write-wins map;
DiscoveryLoader owns its own owned-set bookkeeping so re-running discovery
only removes elements it itself contributed. Adds ChainLoader for explicit
composition. Manual-over-discovered precedence is preserved via loader
ordering, not a flag on the reference.
Split formatting logic from Reference classes into dedicated formatter classes:
- ToolResultFormatter: Formats tool execution results into Content items
- PromptResultFormatter: Formats prompt results into PromptMessage items
- ResourceResultFormatter: Formats resource results into ResourceContents items
This refactor:
- Eliminates 122 lines of code duplication between ResourceReference and
ResourceTemplateReference (identical formatting logic)
- Improves code organization by separating formatting concerns from
capability reference management
- Makes formatters independently testable and reusable
- Reduces Reference classes by ~450 lines while maintaining all functionality
Changes:
- Create src/Capability/Formatter/* with three formatter classes
- Update Reference classes to delegate to formatters instead of inline logic
- Add comprehensive test coverage for all formatter classes
- All existing tests pass; no behavioral changes
