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/contract.py

@@ -12,7 +12,9 @@ PUBLIC_CLI_WORKSPACE_SUBCOMMANDS = (
     "diff",
     "exec",
     "export",
+    "file",
     "logs",
+    "patch",
     "reset",
     "service",
     "shell",
@@ -23,6 +25,8 @@ PUBLIC_CLI_WORKSPACE_SUBCOMMANDS = (
     "sync",
 )
 PUBLIC_CLI_WORKSPACE_DISK_SUBCOMMANDS = ("export", "list", "read")
+PUBLIC_CLI_WORKSPACE_FILE_SUBCOMMANDS = ("list", "read", "write")
+PUBLIC_CLI_WORKSPACE_PATCH_SUBCOMMANDS = ("apply",)
 PUBLIC_CLI_WORKSPACE_SERVICE_SUBCOMMANDS = ("list", "logs", "start", "status", "stop")
 PUBLIC_CLI_WORKSPACE_SHELL_SUBCOMMANDS = ("close", "open", "read", "signal", "write")
 PUBLIC_CLI_WORKSPACE_SNAPSHOT_SUBCOMMANDS = ("create", "delete", "list")
@@ -44,6 +48,10 @@ PUBLIC_CLI_WORKSPACE_DISK_READ_FLAGS = ("--max-bytes", "--json")
 PUBLIC_CLI_WORKSPACE_EXEC_FLAGS = ("--timeout-seconds", "--secret-env", "--json")
 PUBLIC_CLI_WORKSPACE_DIFF_FLAGS = ("--json",)
 PUBLIC_CLI_WORKSPACE_EXPORT_FLAGS = ("--output", "--json")
+PUBLIC_CLI_WORKSPACE_FILE_LIST_FLAGS = ("--recursive", "--json")
+PUBLIC_CLI_WORKSPACE_FILE_READ_FLAGS = ("--max-bytes", "--json")
+PUBLIC_CLI_WORKSPACE_FILE_WRITE_FLAGS = ("--text", "--json")
+PUBLIC_CLI_WORKSPACE_PATCH_APPLY_FLAGS = ("--patch", "--json")
 PUBLIC_CLI_WORKSPACE_RESET_FLAGS = ("--snapshot", "--json")
 PUBLIC_CLI_WORKSPACE_SERVICE_LIST_FLAGS = ("--json",)
 PUBLIC_CLI_WORKSPACE_SERVICE_LOGS_FLAGS = ("--tail-lines", "--all", "--json")
@@ -90,6 +98,7 @@ PUBLIC_CLI_RUN_FLAGS = (
 )
 
 PUBLIC_SDK_METHODS = (
+    "apply_workspace_patch",
     "close_shell",
     "create_server",
     "create_snapshot",
@@ -108,6 +117,7 @@ PUBLIC_SDK_METHODS = (
     "list_services",
     "list_snapshots",
     "list_workspace_disk",
+    "list_workspace_files",
     "logs_service",
     "logs_workspace",
     "network_info_vm",
@@ -117,6 +127,7 @@ PUBLIC_SDK_METHODS = (
     "push_workspace_sync",
     "read_shell",
     "read_workspace_disk",
+    "read_workspace_file",
     "reap_expired",
     "reset_workspace",
     "run_in_vm",
@@ -131,6 +142,7 @@ PUBLIC_SDK_METHODS = (
     "stop_vm",
     "stop_workspace",
     "write_shell",
+    "write_workspace_file",
 )
 
 PUBLIC_MCP_TOOLS = (
@@ -165,7 +177,11 @@ PUBLIC_MCP_TOOLS = (
     "workspace_diff",
     "workspace_exec",
     "workspace_export",
+    "workspace_file_list",
+    "workspace_file_read",
+    "workspace_file_write",
     "workspace_logs",
+    "workspace_patch_apply",
     "workspace_reset",
     "workspace_start",
     "workspace_status",