Enhance documentation and update syncback features

- Updated the `audit.md` documentation to clarify the syncback process and the structure of the `FsSnapshot`.
- Revised the `atlas-api.mdc` to reflect changes in the Git metadata handling, including the introduction of a separate endpoint for fetching Git metadata.
- Improved the `atlas-dedup.mdc` to include handling for the reserved name "init" during slugification.
- Enhanced the `atlas-syncback.mdc` to document the new `SyncbackResult` structure and its integration with the syncback process.
- Updated various sections across multiple documentation files to ensure consistency and clarity regarding the project's architecture and API endpoints.

These changes aim to improve the overall understanding of the system and its components, facilitating better usage and integration.

.cursor/rules/atlas.mdc

@@ -30,9 +30,11 @@ Atlas bridges filesystem and Roblox Studio, enabling professional development to
 **Core capabilities:**
 - Filesystem-based development with live sync to Studio
 - Build/upload rbxl/rbxm files from command line
-- Syncback: pull instances from Roblox → filesystem (7.7.0+)
+- Syncback: pull instances from Roblox → filesystem
 - Two-way sync (plugin-based): live bidirectional sync during `atlas serve` sessions
 - Live syncback: one-click full sync from Studio to filesystem during `atlas serve` (no WebSocket connection required)
+- MCP integration: AI agent-facing JSON-RPC layer for programmatic sync, script access, and Studio tool dispatch
+- Scripts-only mode (`syncScriptsOnly`): sync only script instances, ignore everything else
 
 ### Two-Way Sync Strategy
 
@@ -49,7 +51,7 @@ Atlas bridges filesystem and Roblox Studio, enabling professional development to
 
 ### Three Components
 
-1. **Server/CLI (Rust)** - `src/`, commands: serve, build, upload, syncback, sourcemap
+1. **Server/CLI (Rust)** - `src/`, commands: serve, build, upload, syncback, sourcemap, clone, completions, cursor, studio
 2. **Studio Plugin (Lua)** - `plugin/`, Roact UI, WebSocket sync
 3. **rbx-dom (submodule)** - `rbx-dom/`, Roblox format libraries (binary/XML, types, reflection)
 
@@ -314,7 +316,9 @@ Reconciler.applyPatch(instanceMap, patch)
 
 ```
 src/                     - Rust server/CLI
-  cli/                  - Command implementations
+  cli/                  - Command implementations (serve, build, upload, syncback,
+                          sourcemap, clone, completions, cursor, studio, init,
+                          fmt_project, doc, plugin)
   snapshot/             - Core snapshot system
     matching.rs         - Forward sync matching algorithm
   snapshot_middleware/   - File type handlers
@@ -323,9 +327,14 @@ src/                     - Rust server/CLI
     dedup_suffix.rs     - Dedup cleanup rules
     meta.rs             - Meta file read/write helpers
   web/                  - HTTP/WebSocket server
+    api.rs              - HTTP/WebSocket endpoints
     interface.rs        - Wire types (patches, syncback requests)
+    mcp.rs              - MCP JSON-RPC endpoint, McpState, tool handlers
+    mcp_docs/           - MCP tool description files
   change_processor.rs   - Two-way sync filesystem writer
-  git.rs                - Git integration (changed files, SHA1 hashing, auto-staging)
+  git.rs                - Git integration (CLI-based, changed files, SHA1, auto-staging)
+  logging.rs            - Structured logging, file output to ~/.atlas/logs/, rotation
+  roblox_api.rs         - Roblox auth, place download, experience name lookup
   rojo_ref.rs           - Ref path system (Rojo_Ref_*, RefPathIndex)
   variant_eq.rs         - Property value comparison
 
@@ -336,6 +345,8 @@ plugin/src/             - Lua Studio plugin
     trueEquals.lua      - Shared value equality module
   ChangeBatcher/        - Two-way sync patch creation
     encodeService.lua   - Service-level property encoding for live syncback
+  McpStream.lua         - MCP WebSocket client (ws://host:port/api/mcp/stream)
+  McpTools/             - Studio-side MCP tool dispatch (run_code, insert_model, etc.)
   Config.lua            - Version and protocol config
   PatchTree.lua         - Patch visualization tree (git-based default selections)
   SHA1.luau             - SHA1 hash for git blob format comparison
@@ -368,7 +379,9 @@ rojo-test/              - Test fixtures and utilities
 ## Version Information
 
 - **Protocol version:** 6 (`plugin/src/Config.lua`)
-- **Server/Plugin must match:** MAJOR.MINOR (e.g., 7.7.x works with 7.7.y)
+- **Version matching:** Plugin WebSocket connection requires **exact version match** (`ApiContext.lua`). Live syncback validation uses **MAJOR.MINOR** match (`api.rs`).
+- **Current version:** 8.5.0
+- **Default serve port:** 34873
 - **MSRV:** Rust 1.88
 - **License:** MPL-2.0 (rbx-dom uses MIT)