feat: implement file upload handler and related functionality

- Added file upload handler to process both multipart and raw file uploads.
- Implemented parsing logic for upload requests, including handling file metadata.
- Introduced SaveFileDecodedInput structure for handling decoded file uploads.
- Created unit tests for file upload parsing and validation.

feat: add metadata retry configuration and functionality

- Introduced MetadataRetryConfig to the application configuration.
- Implemented MetadataRetryer to handle retrying metadata extraction for thoughts.
- Added new tool for retrying failed metadata extractions.
- Updated thought metadata structure to include status and timestamps for metadata processing.

fix: enhance metadata normalization and error handling

- Updated metadata normalization functions to track status and errors.
- Improved handling of metadata extraction failures during thought updates and captures.
- Ensured that metadata status is correctly set during various operations.

refactor: streamline file saving logic in FilesTool

- Refactored Save method in FilesTool to utilize new SaveDecoded method.
- Simplified project and thought ID resolution logic during file saving.

internal/tools/reparse_metadata.go

@@ -106,15 +106,18 @@ func (t *ReparseMetadataTool) Handle(ctx context.Context, req *mcp.CallToolReque
 
 			normalizedCurrent := metadata.Normalize(thought.Metadata, t.capture)
 
+			attemptedAt := time.Now().UTC()
 			extracted, extractErr := t.provider.ExtractMetadata(ctx, thought.Content)
 			normalizedTarget := normalizedCurrent
 			if extractErr != nil {
+				normalizedTarget = metadata.MarkMetadataFailed(normalizedCurrent, t.capture, attemptedAt, extractErr)
 				mu.Lock()
 				out.Normalized++
 				mu.Unlock()
 				t.logger.Warn("metadata reparse extract failed, using normalized existing metadata", slog.String("thought_id", thought.ID.String()), slog.String("error", extractErr.Error()))
 			} else {
-				normalizedTarget = metadata.Normalize(extracted, t.capture)
+				normalizedTarget = metadata.MarkMetadataComplete(extracted, t.capture, attemptedAt)
+				normalizedTarget.Attachments = thought.Metadata.Attachments
 				mu.Lock()
 				out.Reparsed++
 				mu.Unlock()