fix: use AbsolutePathBuf for permission profile file roots (#12970)

## Why
`PermissionProfile` should describe filesystem roots as absolute paths
at the type level. Using `PathBuf` in `FileSystemPermissions` made the
shared type too permissive and blurred together three different
deserialization cases:

- skill metadata in `agents/openai.yaml`, where relative paths should
resolve against the skill directory
- app-server API payloads, where callers should have to send absolute
paths
- local tool-call payloads for commands like `shell_command` and
`exec_command`, where `additional_permissions.file_system` may
legitimately be relative to the command `workdir`

This change tightens the shared model without regressing the existing
local command flow.

## What Changed
- changed `protocol::models::FileSystemPermissions` and the app-server
`AdditionalFileSystemPermissions` mirror to use `AbsolutePathBuf`
- wrapped skill metadata deserialization in `AbsolutePathBufGuard`, so
relative permission roots in `agents/openai.yaml` resolve against the
containing skill directory
- kept app-server/API deserialization strict, so relative
`additionalPermissions.fileSystem.*` paths are rejected at the boundary
- restored cwd/workdir-relative deserialization for local tool-call
payloads by parsing `shell`, `shell_command`, and `exec_command`
arguments under an `AbsolutePathBufGuard` rooted at the resolved command
working directory
- simplified runtime additional-permission normalization so it only
canonicalizes and deduplicates absolute roots instead of trying to
recover relative ones later
- updated the app-server schema fixtures, `app-server/README.md`, and
the affected transport/TUI tests to match the final behavior

codex-rs/core/src/tools/runtimes/shell/unix_escalation_tests.rs

@@ -36,7 +36,6 @@ use codex_utils_absolute_path::AbsolutePathBuf;
 use pretty_assertions::assert_eq;
 #[cfg(target_os = "macos")]
 use std::collections::HashMap;
-use std::path::PathBuf;
 use std::time::Duration;
 
 #[test]
@@ -152,7 +151,9 @@ fn shell_request_escalation_execution_is_explicit() {
     let requested_permissions = PermissionProfile {
         file_system: Some(FileSystemPermissions {
             read: None,
-            write: Some(vec![PathBuf::from("./output")]),
+            write: Some(vec![
+                AbsolutePathBuf::from_absolute_path("/tmp/output").unwrap(),
+            ]),
         }),
         ..Default::default()
     };