Architecture
============

Every user-facing operation in ``modalysis`` follows the same six-layer flow:

1. CLI Parser
2. CLI Handler
3. HTTP Client
4. FastAPI Server
5. Core Function

The main CLI entrypoint is ``modalysis.__init__.main``. Subcommands are registered in parser modules with ``set_defaults(func=...)`` and dispatched by ``args.func(args)``.

Design Rules
------------

- Core modules in ``src/modalysis/core`` contain business logic and should not include HTTP or CLI logic.
- Server modules in ``src/modalysis/server`` expose POST endpoints and delegate to core.
- Client modules in ``src/modalysis/client`` send requests to server endpoints.
- CLI handlers in ``src/modalysis/cli/handlers`` parse command arguments and invoke clients.
- CLI parsers in ``src/modalysis/cli/parsers`` define command groups and argument schemas.

Output Convention
-----------------

Tabular processing commands write ``.modalysis`` TSV outputs. Plot commands write ``.png`` files.