MCP server: modelcraft-cli mcp (headless or bridged), read/write roots, end-to-end analysis over MCP (#48)

* io: read and write roots that confine an automation client's file access

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01NmAttHhUZTokgPeEJia8sm

* engine: every file a command reads or writes is checked against the session's roots

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01NmAttHhUZTokgPeEJia8sm

* engine: headless pictures of a session (model, geometry, deformed shape and contours)

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01NmAttHhUZTokgPeEJia8sm

* mcp: MCP server over stdio with headless and connected backends, roots and caps

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01NmAttHhUZTokgPeEJia8sm

* cli: modelcraft-cli mcp [--connect ADDR | --headless] with automation read and write roots

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01NmAttHhUZTokgPeEJia8sm

* mcp: end-to-end analysis of a corpus part over MCP (open, tet mesh, define, solve, probe, render)

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01NmAttHhUZTokgPeEJia8sm

* docs: MCP server (docs/mcp.md), Claude Code setup, roots; architecture, README, roadmap, attribution

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01NmAttHhUZTokgPeEJia8sm

---------

Co-authored-by: jyviko <[email protected]>
Co-authored-by: Claude Opus 5.5 <[email protected]>
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@@ -29,9 +29,9 @@ crates in strictly lower layers.
| L2 | `modelcraft-lbm` | Lattice Boltzmann flow solver on the CPU: D3Q19 two-relaxation-time scheme, bounce-back and slip walls, Zou–He inlets and outlets, obstacles voxelised from the face-tagged surface with exact predicates, momentum-exchange forces per face. Uses `mesh` for the predicates and the boundary surface. | started |
| L3 | `modelcraft-fsi` | Fluid–structure coupling between the L2 solvers (later). | planned |
| L4 | `modelcraft-doc` | The document: geometry, mesh, model, results, history. | planned |
| L5 | `modelcraft-io` | `.modelcraft` files (docs/formats/modelcraft.md): text model definition, binary mesh, geometry references with content hashes, the journal; atomic saves; autosave storage for crash recovery. Bytes in, bytes out; the file system only in `fs` and `recovery`. Result files later. | started |
| L6 | `modelcraft-engine` | Commands (`CommandSpec`), `Session::execute` with rollback and the panic guard, scripts. | started |
| L7 | `modelcraft-ui-egui`, `modelcraft-mcp` | Desktop UI in the Craft family's layout (title bar with quick actions, workspace ribbon from the catalogue, browser, viewport with navigation bar and orientation gizmo, context panel, command search and command line, journal timeline; native file pickers as host services, background opening and solving; results display with legend and probe; offscreen capture of the whole window) and control channel requests (docs/control-protocol.md); MCP server. | ui started |
| L5 | `modelcraft-io` | `.modelcraft` files (docs/formats/modelcraft.md): text model definition, binary mesh, geometry references with content hashes, the journal; atomic saves; autosave storage for crash recovery; read and write roots that confine an automation client's file access (`roots`). Bytes in, bytes out; the file system only in `fs`, `recovery` and `roots`. Result files later. | started |
| L6 | `modelcraft-engine` | Commands (`CommandSpec`), `Session::execute` with rollback and the panic guard, scripts; every file a command names checked against the session's roots (`Session::file_access`); headless pictures of the session (`view`: model, geometry, deformed shape and contours on the CPU rasterizer). | started |
| L7 | `modelcraft-ui-egui`, `modelcraft-mcp` | Desktop UI in the Craft family's layout (title bar with quick actions, workspace ribbon from the catalogue, browser, viewport with navigation bar and orientation gizmo, context panel, command search and command line, journal timeline; native file pickers as host services, background opening and solving; results display with legend and probe; offscreen capture of the whole window) and control channel requests (docs/control-protocol.md); MCP server over stdio (docs/mcp.md): tools over engine commands, a headless session or the running app through its control channel, read and write roots. | ui, mcp started |
| testkit | `modelcraft-testkit` | Test tooling, a dev-dependency only: the meshing test corpus (`tests/corpus/*/recipe.json`, analytic shapes) and its runner (`cargo xtask corpus`). | started |
| apps | `modelcraft`, `modelcraft-cli`, `modelcraft-web` | Desktop, command line, browser. | desktop, cli started |