Add model-native workspace file operations

Remove shell-escaped file mutation from the stable workspace flow by adding explicit file and patch tools across the CLI, SDK, and MCP surfaces.

This adds workspace file list/read/write plus unified text patch application, backed by new guest and manager file primitives that stay scoped to started workspaces and /workspace only. Patch application is preflighted on the host, file writes stay text-only and bounded, and the existing diff/export/reset semantics remain intact.

The milestone also updates the 3.2.0 roadmap, public contract, docs, examples, and versioning, and includes focused coverage for the new helper module and dispatch paths.

Validation:
- uv lock
- UV_CACHE_DIR=.uv-cache make check
- UV_CACHE_DIR=.uv-cache make dist-check
- real guest-backed smoke for workspace file read, patch apply, exec, export, and delete

src/pyro_mcp/vm_environments.py

@@ -19,7 +19,7 @@ from typing import Any
 from pyro_mcp.runtime import DEFAULT_PLATFORM, RuntimePaths
 
 DEFAULT_ENVIRONMENT_VERSION = "1.0.0"
-DEFAULT_CATALOG_VERSION = "3.1.0"
+DEFAULT_CATALOG_VERSION = "3.2.0"
 OCI_MANIFEST_ACCEPT = ", ".join(
     (
         "application/vnd.oci.image.index.v1+json",