Merge documented PreToolUse base into PermissionRequest stack

codex-rs/core/src/tools/handlers/apply_patch.rs

@@ -325,6 +325,9 @@ impl ToolHandler for ApplyPatchHandler {
         })
     }
 
+    // Hooks expose apply_patch through the stable `{ "command": ... }` shape,
+    // while the underlying tool stores the patch as either the function
+    // argument `input` or freeform custom-tool input.
     fn with_updated_hook_input(
         &self,
         mut invocation: ToolInvocation,

codex-rs/core/src/tools/handlers/mcp.rs

@@ -48,6 +48,9 @@ impl ToolHandler for McpHandler {
         })
     }
 
+    // MCP hooks expose the full arguments object, so rewrites replace the
+    // serialized raw argument payload wholesale rather than patching one
+    // handler-owned field.
     fn with_updated_hook_input(
         &self,
         mut invocation: ToolInvocation,

codex-rs/core/src/tools/handlers/shell.rs

@@ -379,6 +379,8 @@ impl ToolHandler for LocalShellHandler {
         })
     }
 
+    // Hooks see a joined shell command string, but local_shell stores argv.
+    // Split on the way back in to invert the hook-facing representation.
     fn with_updated_hook_input(
         &self,
         mut invocation: ToolInvocation,

codex-rs/core/src/tools/handlers/unified_exec.rs

@@ -164,6 +164,8 @@ impl ToolHandler for ExecCommandHandler {
             })
     }
 
+    // Hooks normalize Bash-like tools to `{ "command": ... }`, while the
+    // exec_command wire schema still names the field `cmd`.
     fn with_updated_hook_input(
         &self,
         mut invocation: ToolInvocation,