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 <noreply@anthropic.com>
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 <noreply@anthropic.com>
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 <noreply@anthropic.com>
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 <noreply@anthropic.com>
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 <noreply@anthropic.com>
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 <noreply@anthropic.com>
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 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01NmAttHhUZTokgPeEJia8sm

---------

Co-authored-by: jyviko <2501648+jyviko@users.noreply.github.com>
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>

crates/io/src/lib.rs

@@ -17,14 +17,15 @@
 //! The same model always gives the same bytes. Reading treats the file as hostile: every size is
 //! capped before anything is allocated, every part's checksum is verified, and the model is
 //! rebuilt through the same checked methods commands use, so a file cannot hold what commands
-//! would refuse. Reading and writing work on bytes (they build for the browser); only [`fs`] and
-//! [`recovery`] touch the file system.
+//! would refuse. Reading and writing work on bytes (they build for the browser); only [`fs`],
+//! [`recovery`] and [`roots`] touch the file system.
 #![deny(clippy::unwrap_used, clippy::expect_used, clippy::panic, clippy::unimplemented, clippy::todo, clippy::unreachable)]
 #![forbid(unsafe_code)]
 
 pub mod fs;
 pub mod mesh;
 pub mod recovery;
+pub mod roots;
 
 use std::collections::BTreeMap;
 use std::io::{Cursor, Read, Write};
@@ -74,6 +75,9 @@ pub enum Error {
     /// The file system refused.
     #[error("{0}")]
     Io(String),
+    /// The path lies outside the folders file access is confined to ([`roots::Roots`]).
+    #[error("{0}")]
+    Refused(String),
 }
 
 pub type Result<T> = std::result::Result<T, Error>;