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/update.go

@@ -4,6 +4,7 @@ import (
 	"context"
 	"log/slog"
 	"strings"
+	"time"
 
 	"github.com/modelcontextprotocol/go-sdk/mcp"
 
@@ -64,8 +65,9 @@ func (t *UpdateTool) Handle(ctx context.Context, _ *mcp.CallToolRequest, in Upda
 		extracted, extractErr := t.provider.ExtractMetadata(ctx, content)
 		if extractErr != nil {
 			t.log.Warn("metadata extraction failed during update, keeping current metadata", slog.String("error", extractErr.Error()))
+			mergedMetadata = metadata.MarkMetadataFailed(mergedMetadata, t.capture, time.Now().UTC(), extractErr)
 		} else {
-			mergedMetadata = metadata.Normalize(extracted, t.capture)
+			mergedMetadata = metadata.MarkMetadataComplete(extracted, t.capture, time.Now().UTC())
 			mergedMetadata.Attachments = current.Metadata.Attachments
 		}
 	}