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/app-server-protocol/schema/json/CommandExecutionRequestApprovalParams.json

@@ -1,11 +1,15 @@
 {
   "$schema": "http://json-schema.org/draft-07/schema#",
   "definitions": {
+    "AbsolutePathBuf": {
+      "description": "A path that is guaranteed to be absolute and normalized (though it is not guaranteed to be canonicalized or exist on the filesystem).\n\nIMPORTANT: When deserializing an `AbsolutePathBuf`, a base path must be set using [AbsolutePathBufGuard::new]. If no base path is set, the deserialization will fail unless the path being deserialized is already absolute.",
+      "type": "string"
+    },
     "AdditionalFileSystemPermissions": {
       "properties": {
         "read": {
           "items": {
-            "type": "string"
+            "$ref": "#/definitions/AbsolutePathBuf"
           },
           "type": [
             "array",
@@ -14,7 +18,7 @@
         },
         "write": {
           "items": {
-            "type": "string"
+            "$ref": "#/definitions/AbsolutePathBuf"
           },
           "type": [
             "array",

codex-rs/app-server-protocol/schema/json/EventMsg.json

@@ -3411,7 +3411,7 @@
       "properties": {
         "read": {
           "items": {
-            "type": "string"
+            "$ref": "#/definitions/AbsolutePathBuf"
           },
           "type": [
             "array",
@@ -3420,7 +3420,7 @@
         },
         "write": {
           "items": {
-            "type": "string"
+            "$ref": "#/definitions/AbsolutePathBuf"
           },
           "type": [
             "array",

codex-rs/app-server-protocol/schema/json/ServerRequest.json

@@ -1,11 +1,15 @@
 {
   "$schema": "http://json-schema.org/draft-07/schema#",
   "definitions": {
+    "AbsolutePathBuf": {
+      "description": "A path that is guaranteed to be absolute and normalized (though it is not guaranteed to be canonicalized or exist on the filesystem).\n\nIMPORTANT: When deserializing an `AbsolutePathBuf`, a base path must be set using [AbsolutePathBufGuard::new]. If no base path is set, the deserialization will fail unless the path being deserialized is already absolute.",
+      "type": "string"
+    },
     "AdditionalFileSystemPermissions": {
       "properties": {
         "read": {
           "items": {
-            "type": "string"
+            "$ref": "#/definitions/AbsolutePathBuf"
           },
           "type": [
             "array",
@@ -14,7 +18,7 @@
         },
         "write": {
           "items": {
-            "type": "string"
+            "$ref": "#/definitions/AbsolutePathBuf"
           },
           "type": [
             "array",

codex-rs/app-server-protocol/schema/json/codex_app_server_protocol.schemas.json

@@ -5,7 +5,7 @@
       "properties": {
         "read": {
           "items": {
-            "type": "string"
+            "$ref": "#/definitions/AbsolutePathBuf"
           },
           "type": [
             "array",
@@ -14,7 +14,7 @@
         },
         "write": {
           "items": {
-            "type": "string"
+            "$ref": "#/definitions/AbsolutePathBuf"
           },
           "type": [
             "array",
@@ -4722,7 +4722,7 @@
       "properties": {
         "read": {
           "items": {
-            "type": "string"
+            "$ref": "#/definitions/AbsolutePathBuf"
           },
           "type": [
             "array",
@@ -4731,7 +4731,7 @@
         },
         "write": {
           "items": {
-            "type": "string"
+            "$ref": "#/definitions/AbsolutePathBuf"
           },
           "type": [
             "array",