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/mcpserver/server.go

@@ -11,27 +11,28 @@ import (
 )
 
 type ToolSet struct {
-	Capture     *tools.CaptureTool
-	Search      *tools.SearchTool
-	List        *tools.ListTool
-	Stats       *tools.StatsTool
-	Get         *tools.GetTool
-	Update      *tools.UpdateTool
-	Delete      *tools.DeleteTool
-	Archive     *tools.ArchiveTool
-	Projects    *tools.ProjectsTool
-	Context     *tools.ContextTool
-	Recall      *tools.RecallTool
-	Summarize   *tools.SummarizeTool
-	Links       *tools.LinksTool
-	Files       *tools.FilesTool
-	Backfill    *tools.BackfillTool
-	Reparse     *tools.ReparseMetadataTool
-	Household   *tools.HouseholdTool
-	Maintenance *tools.MaintenanceTool
-	Calendar    *tools.CalendarTool
-	Meals       *tools.MealsTool
-	CRM         *tools.CRMTool
+	Capture       *tools.CaptureTool
+	Search        *tools.SearchTool
+	List          *tools.ListTool
+	Stats         *tools.StatsTool
+	Get           *tools.GetTool
+	Update        *tools.UpdateTool
+	Delete        *tools.DeleteTool
+	Archive       *tools.ArchiveTool
+	Projects      *tools.ProjectsTool
+	Context       *tools.ContextTool
+	Recall        *tools.RecallTool
+	Summarize     *tools.SummarizeTool
+	Links         *tools.LinksTool
+	Files         *tools.FilesTool
+	Backfill      *tools.BackfillTool
+	Reparse       *tools.ReparseMetadataTool
+	RetryMetadata *tools.RetryMetadataTool
+	Household     *tools.HouseholdTool
+	Maintenance   *tools.MaintenanceTool
+	Calendar      *tools.CalendarTool
+	Meals         *tools.MealsTool
+	CRM           *tools.CRMTool
 }
 
 func New(cfg config.MCPConfig, toolSet ToolSet) http.Handler {
@@ -150,6 +151,11 @@ func New(cfg config.MCPConfig, toolSet ToolSet) http.Handler {
 		Description: "Re-extract and normalize metadata for stored thoughts from their content.",
 	}, toolSet.Reparse.Handle)
 
+	addTool(server, &mcp.Tool{
+		Name:        "retry_failed_metadata",
+		Description: "Retry metadata extraction for thoughts still marked pending or failed.",
+	}, toolSet.RetryMetadata.Handle)
+
 	// Household Knowledge
 	addTool(server, &mcp.Tool{
 		Name:        "add_household_item",