Your proposed structure for the API sounds solid and modular, making it easier to manage files and their relationships with other data. Here’s a breakdown of how this can work and how it could be used with an iOS shortcut or a custom application:

API Structure
File Management Endpoints:

POST /file: Accepts a file upload and returns a unique identifier (ID) for that file.
PUT /file/{id}: Updates the metadata of the file identified by {id}.
DELETE /file/{id}: Deletes the file and its associated metadata from the database.
Data Ingress Endpoint:

POST /ingress: Accepts a JSON body containing references (IDs) to files and other necessary data, linking them in the database as needed.
Using with iOS Shortcuts
You can create shortcuts to interact with your API endpoints without the need for a full-fledged application. Here's how:

File Upload Shortcut:

Use the "Get File" action to select a file from the device.
Use the "Post" action to send a multipart/form-data request to the /file endpoint.
Parse the response to get the returned file ID.
Data Ingress Shortcut:

Use the "Ask for Input" action to gather the necessary fields for the ingress (like instructions, category, etc.) and the file ID(s).
Use another "Post" action to send this data to the /ingress endpoint as JSON.
Developing a CLI Tool
A CLI tool could also be developed for easier interaction with your API. This tool could:

Upload Files: Handle file uploads and return file IDs.
Link Data: Accept user input for instructions, category, and linked file IDs, then submit this data to the /ingress endpoint.
Additional Considerations
Error Handling: Ensure that both the upload and ingress endpoints handle errors gracefully and provide meaningful messages.
Documentation: Create clear API documentation to guide users in constructing requests correctly, whether they are using a shortcut, CLI, or custom application.
Authentication: Consider adding authentication to your API endpoints for security, especially if sensitive data is being handled.
This approach gives you the flexibility to support various clients, streamline interactions, and keep the server-side implementation clean and manageable. Would you like more specifics on any part of this setup?
