docs: fix architecture tree duplication and add missing MCP fields (#320)

* Initial plan

* docs: fix architecture tree and MCP server docs

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Co-authored-by: jamesadevine <4742697+jamesadevine@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: jamesadevine <4742697+jamesadevine@users.noreply.github.com>

Author: Copilot

AGENTS.md

@@ -22,8 +22,7 @@ Alongside the correctly generated pipeline yaml, an agent file is generated from
 │   ├── main.rs           # Entry point with clap CLI
 │   ├── allowed_hosts.rs  # Core network allowlist definitions
 │   ├── ecosystem_domains.rs # Ecosystem domain lookups (python, rust, node, etc.)
-│   ├── data/
-│   │   └── ecosystem_domains.json # Ecosystem domain lists (synced from gh-aw)
+│   ├── engine.rs         # Engine enum, CLI params, model/version defaults
 │   ├── compile/          # Pipeline compilation module
 │   │   ├── mod.rs        # Module entry point and Compiler trait
 │   │   ├── common.rs     # Shared helpers across targets

README.md

@@ -328,6 +328,20 @@ mcp-servers:
     container: "node:20-slim"
     entrypoint: "node"
     entrypoint-args: ["path/to/mcp-server.js"]
+    # args: additional Docker runtime arguments inserted before the image name
+    #   (e.g. ["--memory", "512m"]).  Dangerous flags like --privileged trigger
+    #   a compile-time warning.
+    args: []
+    # mounts: volume mounts in "source:dest:mode" format
+    mounts:
+      - "/host/data:/app/data:ro"
+    # env: environment variables for the MCP container process.
+    #   Use "" (empty string) as the value to forward the variable from the
+    #   pipeline environment (passthrough); supply a literal string for static
+    #   values.
+    env:
+      MY_SECRET: ""          # passthrough from pipeline env
+      STATIC_VALUE: "hello"  # literal value
     allowed:
       - search
       - analyze