os/mac/{keg,mach}: fix cache invalidation

We were rewriting dylib IDs and install names using `MachO::Tools`,
which doesn't update the state of the file in memory. This leads to
those changes being undone when we call `change_rpath`.

We fix this by making sure the state of the file in memory always
matches the state of file on disk.

Closes Homebrew#12832.

Library/Homebrew/os/mac/keg.rb

@@ -7,7 +7,7 @@ def change_dylib_id(id, file)
 
     @require_relocation = true
     odebug "Changing dylib ID of #{file}\n  from #{file.dylib_id}\n    to #{id}"
-    MachO::Tools.change_dylib_id(file, id, strict: false)
+    file.change_dylib_id(id, strict: false)
     apply_ad_hoc_signature(file)
   rescue MachO::MachOError
     onoe <<~EOS
@@ -23,7 +23,7 @@ def change_install_name(old, new, file)
 
     @require_relocation = true
     odebug "Changing install name in #{file}\n  from #{old}\n    to #{new}"
-    MachO::Tools.change_install_name(file, old, new, strict: false)
+    file.change_install_name(old, new, strict: false)
     apply_ad_hoc_signature(file)
   rescue MachO::MachOError
     onoe <<~EOS

Library/Homebrew/os/mac/mach.rb

@@ -64,6 +64,16 @@ def delete_rpath(rpath, **options)
     macho.write!
   end
 
+  def change_dylib_id(id, **options)
+    macho.change_dylib_id(id, options)
+    macho.write!
+  end
+
+  def change_install_name(old, new, **options)
+    macho.change_install_name(old, new, options)
+    macho.write!
+  end
+
   def dynamically_linked_libraries(except: :none)
     lcs = macho.dylib_load_commands.reject { |lc| lc.type == except }